[ { "id": "Q14004-1.291.291", "start_pos": 291, "end_pos": 291, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14004", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKDRDSKAHRSRTKSSKEPP", "down_seq": "AYKEPPKAYREDKTEPKAYR", "snv": [ { "evidence": [ { "id": "Q14004", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004" } ], "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": "7", "chr_pos": "39951513", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S291", "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": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q14004-1.303.303", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.303.303", "start_pos": 303, "end_pos": 303, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs368100231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368100231", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368100231", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs368100231", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs368100231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368100231", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs368100231", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368100231#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs368100231", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368100231", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TKSSKEPPSAYKEPPKAYRE", "down_seq": "KTEPKAYRRRRSLSPLGGRD", "snv": [ { "evidence": [ { "id": "rs368100231", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368100231" }, { "id": "rs368100231", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs368100231" }, { "id": "rs368100231", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368100231" }, { "id": "rs368100231", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368100231#frequency_tab" }, { "id": "rs368100231", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368100231" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DKT->NKT).", "chr_id": "7", "chr_pos": "39951548", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000588697", "site_lbl": "D303", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q14004-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.315.315", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.323.323", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.323.323", "start_pos": 323, "end_pos": 323, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1405991709", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1405991709", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1405991709", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1405991709", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1405991709", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1405991709", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DKTEPKAYRRRRSLSPLGGR", "down_seq": "DSPVSHRASQSLRSRKSPSP", "snv": [ { "evidence": [ { "id": "rs1405991709", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1405991709" }, { "id": "rs1405991709", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1405991709" }, { "id": "rs1405991709", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1405991709" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "7", "chr_pos": "39951608", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D323", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14004-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14004-1.315.315", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14004-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14004-1.328.328", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.337.337", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14004-1.342.342", "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": "Q14004-1.369.369", "start_pos": 369, "end_pos": 369, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1423143048", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1423143048", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1423143048", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1423143048#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPYSRRLPRSPSPYSRRRSP", "down_seq": "YSRHSSYERGGDVSPSPYSS", "snv": [ { "evidence": [ { "id": "rs1423143048", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1423143048" }, { "id": "rs1423143048", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1423143048#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 (SYS->NYS).", "chr_id": "7", "chr_pos": "39951747", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S369", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q14004-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.383.383", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14004-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.389.389", "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": "Q14004-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2116072661", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2116072661", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2116072661", "url": "https://www.ensembl.org/id/rs2116072661", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PYSRRRSPSYSRHSSYERGG", "down_seq": "VSPSPYSSSSWRRSRSPYSP", "snv": [ { "evidence": [ { "id": "rs2116072661", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2116072661" }, { "id": "rs2116072661", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2116072661" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DVS->NVS).", "chr_id": "7", "chr_pos": "39951782", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D381", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14004-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.369.369", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.383.383", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14004-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.395.395", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14004-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q14004-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14004-1.400.400", "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": "Q14004-1.388.388", "start_pos": 388, "end_pos": 388, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1203101412", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1203101412", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1203101412", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1203101412#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1203101412", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1203101412", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSYSRHSSYERGGDVSPSPY", "down_seq": "SSSWRRSRSPYSPVLRRSGK", "snv": [ { "evidence": [ { "id": "rs1203101412", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1203101412" }, { "id": "rs1203101412", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1203101412#frequency_tab" }, { "id": "rs1203101412", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1203101412" } ], "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 (SSS->NSS).", "chr_id": "7", "chr_pos": "39951804", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S388", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14004-1.369.369", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14004-1.383.383", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14004-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14004-1.395.395", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.400.400", "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": "Q14004-1.389.389", "start_pos": 389, "end_pos": 389, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2116073238", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2116073238", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2116073238", "url": "https://www.ensembl.org/id/rs2116073238", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SYSRHSSYERGGDVSPSPYS", "down_seq": "SSWRRSRSPYSPVLRRSGKS", "snv": [ { "evidence": [ { "id": "rs2116073238", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2116073238" }, { "id": "rs2116073238", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2116073238" } ], "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 (SSS->NSS).", "chr_id": "7", "chr_pos": "39951807", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S389", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14004-1.369.369", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14004-1.383.383", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14004-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.395.395", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.400.400", "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": "Q14004-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1787120811", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1787120811", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1787120811", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1787120811#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MP", "down_seq": "SSDTALGGGGGLSWAEKKLE", "snv": [ { "evidence": [ { "id": "rs1787120811", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1787120811" }, { "id": "rs1787120811", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1787120811#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 (SSS->NSS).", "chr_id": "7", "chr_pos": "39950649", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S3", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "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": "Q14004-1.411.411", "start_pos": 411, "end_pos": 411, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2116262587", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2116262587", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2116262587", "url": "https://www.ensembl.org/id/rs2116262587", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SWRRSRSPYSPVLRRSGKSR", "down_seq": "RSPYSSRHSRSRSRHRLSRS", "snv": [ { "evidence": [ { "id": "rs2116262587", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2116262587" }, { "id": "rs2116262587", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2116262587" } ], "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 (SRS->NRS).", "chr_id": "7", "chr_pos": "39987619", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S411", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14004-1.395.395", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14004-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.400.400", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14004-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.431.431", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.427.427", "start_pos": 427, "end_pos": 427, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14004", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GKSRSRSPYSSRHSRSRSRH", "down_seq": "LSRSRSRHSSISPSTLTLKS", "snv": [ { "evidence": [ { "id": "Q14004", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004" } ], "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": "7", "chr_pos": "39987667", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R427", "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": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14004-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14004-1.431.431", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.437.437", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14004-1.444.444", "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": "Q14004-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1333323434", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1333323434", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1333323434", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1333323434", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "YSSRHSRSRSRHRLSRSRSR", "down_seq": "SSISPSTLTLKSSLAAELNK", "snv": [ { "evidence": [ { "id": "rs1333323434", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1333323434" }, { "id": "rs1333323434", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1333323434" } ], "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": "7", "chr_pos": "39987690", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H435", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14004-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14004-1.431.431", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.437.437", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.444.444", "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": "Q14004-1.456.456", "start_pos": 456, "end_pos": 456, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200938169", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200938169", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200938169", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200938169", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200938169", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200938169#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200938169", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200938169", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SSISPSTLTLKSSLAAELNK", "down_seq": "KKARAAEAARAAEAAKAAEA", "snv": [ { "evidence": [ { "id": "rs200938169", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200938169" }, { "id": "rs200938169", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200938169" }, { "id": "rs200938169", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200938169#frequency_tab" }, { "id": "rs200938169", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200938169" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKN->NKS).", "chr_id": "7", "chr_pos": "39987754", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N456", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14004-1.437.437", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.444.444", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.458.458", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14004", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ISPSTLTLKSSLAAELNKNK", "down_seq": "ARAAEAARAAEAAKAAEATK", "snv": [ { "evidence": [ { "id": "Q14004", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKK->NKT).", "chr_id": "7", "chr_pos": "39987760", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K458", "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": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14004-1.444.444", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.456.456", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.505.505", "start_pos": 505, "end_pos": 505, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778059575", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778059575", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778059575", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778059575", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778059575", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778059575#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778059575", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778059575", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KAAKASNTSTPTKGNTETSA", "down_seq": "ASQTNHVKDVKKIKIEHAPS", "snv": [ { "evidence": [ { "id": "rs778059575", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778059575" }, { "id": "rs778059575", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778059575" }, { "id": "rs778059575", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778059575#frequency_tab" }, { "id": "rs778059575", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778059575" } ], "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": "39987901", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S505", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14004-1.490.490", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.493.493", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.525.525", "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": "Q14004-1.553.553", "start_pos": 553, "end_pos": 553, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767473614", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767473614", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767473614", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767473614", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767473614", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767473614", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KNDKAKTKPPLQVTKVENNL", "down_seq": "VDKATKKAVIVGKESKSAAT", "snv": [ { "evidence": [ { "id": "rs767473614", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767473614" }, { "id": "rs767473614", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767473614" }, { "id": "rs767473614", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767473614" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLI->NLT).", "chr_id": "7", "chr_pos": "39988045", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I553", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q14004-1.566.566", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.566.566", "start_pos": 566, "end_pos": 566, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14004", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1348083600", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348083600", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1348083600", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1348083600", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TKVENNLIVDKATKKAVIVG", "down_seq": "ESKSAATKEESVSLKEKTKP", "snv": [ { "evidence": [ { "id": "Q14004", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004" }, { "id": "rs1348083600", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348083600" }, { "id": "rs1348083600", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1348083600" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KES->NES).", "chr_id": "7", "chr_pos": "39988085", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K566", "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": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14004-1.553.553", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.668.668", "start_pos": 668, "end_pos": 668, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14004", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "DLPLPPELPGGDDLSKSPEE", "down_seq": "KTATQLHSKRRPKICGPRYG", "snv": [ { "evidence": [ { "id": "Q14004", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KKT->NKT).", "chr_id": "7", "chr_pos": "39997626", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K668", "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": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q14004-1.662.662", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14004-1.664.664", "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": "Q14004-1.725.725", "start_pos": 725, "end_pos": 725, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781506575", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781506575", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781506575", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781506575", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781506575", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781506575", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FDIIGIIGEGTYGQVYKARD", "down_seq": "DTGEMVALKKVRLDNEKEGF", "snv": [ { "evidence": [ { "id": "rs781506575", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781506575" }, { "id": "rs781506575", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781506575" }, { "id": "rs781506575", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781506575" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KDT->NDT).", "chr_id": "7", "chr_pos": "39999493", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K725", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q14004-1.737.737", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.737.737", "start_pos": 737, "end_pos": 737, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14004", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GQVYKARDKDTGEMVALKKV", "down_seq": "LDNEKEGFPITAIREIKILR", "snv": [ { "evidence": [ { "id": "Q14004", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "40001887", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R737", "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:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q14004-1.725.725", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14004-1.761.761", "start_pos": 761, "end_pos": 761, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777432797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777432797", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777432797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777432797", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777432797", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777432797", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "EKEGFPITAIREIKILRQLT", "down_seq": "QSIINMKEIVTDKEDALDFK", "snv": [ { "evidence": [ { "id": "rs777432797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777432797" }, { "id": "rs777432797", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777432797" }, { "id": "rs777432797", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777432797" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HQS->NQS).", "chr_id": "7", "chr_pos": "40001959", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H761", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "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": "Q14004-1.792.792", "start_pos": 792, "end_pos": 792, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14004", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "TDKEDALDFKKDKGAFYLVF", "down_seq": "YMDHDLMGLLESGLVHFNEN", "snv": [ { "evidence": [ { "id": "Q14004", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14004" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "7", "chr_pos": "40045856", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E792", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "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": "Q14004-1.1048.1048", "start_pos": 1048, "end_pos": 1048, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "QKQMGMTDDVSTIKAPRKDL", "down_seq": "LGLDDSRTNTPQGVLPSSQL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser1048" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q14004-1.1052.1052", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.1054.1054", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.1056.1056", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.1058.1058", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q14004-1.1066.1066", "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": "Q14004-1.1054.1054", "start_pos": 1054, "end_pos": 1054, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TDDVSTIKAPRKDLSLGLDD", "down_seq": "RTNTPQGVLPSSQLKSQGSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser1054" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q14004-1.1048.1048", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.1052.1052", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.1056.1056", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14004-1.1058.1058", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.1066.1066", "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": "Q14004-1.1056.1056", "start_pos": 1056, "end_pos": 1056, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DVSTIKAPRKDLSLGLDDSR", "down_seq": "NTPQGVLPSSQLKSQGSSNV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Thr1056" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14004-1.1048.1048", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14004-1.1052.1052", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.1054.1054", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.1058.1058", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.1066.1066", "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": "Q14004-1.1058.1058", "start_pos": 1058, "end_pos": 1058, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "STIKAPRKDLSLGLDDSRTN", "down_seq": "PQGVLPSSQLKSQGSSNVAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Thr1058" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q14004-1.1048.1048", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14004-1.1052.1052", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14004-1.1054.1054", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.1056.1056", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.1066.1066", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14004-1.1077.1077", "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": "Q14004-1.1066.1066", "start_pos": 1066, "end_pos": 1066, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "A0A2R8Y4Z0", "url": "https://www.uniprot.org/uniprotkb/A0A2R8Y4Z0" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLSLGLDDSRTNTPQGVLPS", "down_seq": "QLKSQGSSNVAPVKTGPGQH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ], "site_lbl": "Ser1066" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q14004-1.1048.1048", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14004-1.1052.1052", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.1054.1054", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14004-1.1056.1056", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14004-1.1058.1058", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.1077.1077", "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": "Q14004-1.1143.1143", "start_pos": 1143, "end_pos": 1143, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QQQLNKINLPAGILATGEKQ", "down_seq": "DPSTPQQESSKPLGGIQPSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Thr1143" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q14004-1.1146.1146", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14004-1.1147.1147", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.1153.1153", "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": "Q14004-1.1146.1146", "start_pos": 1146, "end_pos": 1146, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "journal": "Proteomics", "date": "2008", "authors": "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316", "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": "LNKINLPAGILATGEKQTDP", "down_seq": "TPQQESSKPLGGIQPSSQTI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser1146" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q14004-1.1143.1143", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14004-1.1147.1147", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14004-1.1153.1153", "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": "Q14004-1.1147.1147", "start_pos": 1147, "end_pos": 1147, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NKINLPAGILATGEKQTDPS", "down_seq": "PQQESSKPLGGIQPSSQTIQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Thr1147" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q14004-1.1143.1143", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14004-1.1146.1146", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.1153.1153", "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": "Q14004-1.1246.1246", "start_pos": 1246, "end_pos": 1246, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.", "journal": "Journal of proteome research", "date": "2008", "authors": "Tsai CF, Wang YT, Chen YR, Lai CY, Lin PY, Pan KT, Chen JY, Khoo KH, Chen YJ", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TPVSGQDDLIQHQDMRILEL", "down_seq": "PEPDRPRILPPDQRPPEPPE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1246" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.1277.1277", "start_pos": 1277, "end_pos": 1277, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "PDQRPPEPPEPPPVTEEDLD", "down_seq": "RTENQHVPTTSSSLTDPHAG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr1277" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q14004-1.1279.1279", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.1286.1286", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.1287.1287", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.1288.1288", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.1289.1289", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14004-1.1290.1290", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14004-1.1292.1292", "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": "Q14004-1.1471.1471", "start_pos": 1471, "end_pos": 1471, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HPLPAKMHNYNYGGNLQENP", "down_seq": "GPSLMHGQTWTSPAQGPGYS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser1471" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q14004-1.1461.1461", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14004-1.1463.1463", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14004-1.1470.1470", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.1491.1491", "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": "Q14004-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "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": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPPKAYREDKTEPKAYRRRR", "down_seq": "LSPLGGRDDSPVSHRASQSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "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": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser315" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q14004-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14004-1.328.328", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.317.317", "start_pos": 317, "end_pos": 317, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "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": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PKAYREDKTEPKAYRRRRSL", "down_seq": "PLGGRDDSPVSHRASQSLRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "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": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser317" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14004-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.315.315", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.328.328", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.337.337", "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": "Q14004-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "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": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TEPKAYRRRRSLSPLGGRDD", "down_seq": "PVSHRASQSLRSRKSPSPAG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "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": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser325" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q14004-1.315.315", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14004-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14004-1.328.328", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.337.337", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14004-1.342.342", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.328.328", "start_pos": 328, "end_pos": 328, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KAYRRRRSLSPLGGRDDSPV", "down_seq": "HRASQSLRSRKSPSPAGGGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser328" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14004-1.315.315", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14004-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14004-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.337.337", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.342.342", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.348.348", "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": "Q14004-1.337.337", "start_pos": 337, "end_pos": 337, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "SPLGGRDDSPVSHRASQSLR", "down_seq": "RKSPSPAGGGSSPYSRRLPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser337" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14004-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14004-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.328.328", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14004-1.342.342", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.348.348", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.351.351", "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": "Q14004-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGRDDSPVSHRASQSLRSRK", "down_seq": "PSPAGGGSSPYSRRLPRSPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser340" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14004-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q14004-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.328.328", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14004-1.337.337", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.342.342", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.348.348", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q14004-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.360.360", "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": "Q14004-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RDDSPVSHRASQSLRSRKSP", "down_seq": "PAGGGSSPYSRRLPRSPSPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser342" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14004-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q14004-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14004-1.328.328", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14004-1.337.337", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.348.348", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14004-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q14004-1.360.360", "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": "Q14004-1.348.348", "start_pos": 348, "end_pos": 348, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SHRASQSLRSRKSPSPAGGG", "down_seq": "SPYSRRLPRSPSPYSRRRSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "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": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser348" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14004-1.328.328", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.337.337", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14004-1.342.342", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14004-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14004-1.367.367", "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": "Q14004-1.349.349", "start_pos": 349, "end_pos": 349, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "HRASQSLRSRKSPSPAGGGS", "down_seq": "PYSRRLPRSPSPYSRRRSPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "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": "Ser349" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q14004-1.337.337", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14004-1.342.342", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14004-1.348.348", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q14004-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14004-1.369.369", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.351.351", "start_pos": 351, "end_pos": 351, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "ASQSLRSRKSPSPAGGGSSP", "down_seq": "SRRLPRSPSPYSRRRSPSYS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr351" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14004-1.337.337", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.342.342", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14004-1.348.348", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14004-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14004-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q14004-1.369.369", "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": "Q14004-1.358.358", "start_pos": 358, "end_pos": 358, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKSPSPAGGGSSPYSRRLPR", "down_seq": "PSPYSRRRSPSYSRHSSYER", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser358" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q14004-1.342.342", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14004-1.348.348", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14004-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.369.369", "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": "Q14004-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPSPAGGGSSPYSRRLPRSP", "down_seq": "PYSRRRSPSYSRHSSYERGG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser360" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14004-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q14004-1.342.342", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.348.348", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14004-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14004-1.369.369", "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": "Q14004-1.367.367", "start_pos": 367, "end_pos": 367, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSSPYSRRLPRSPSPYSRRR", "down_seq": "PSYSRHSSYERGGDVSPSPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ], "site_lbl": "Ser367" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14004-1.348.348", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q14004-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q14004-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14004-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.369.369", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14004-1.383.383", "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": "Q14004-1.383.383", "start_pos": 383, "end_pos": 383, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "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": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRRRSPSYSRHSSYERGGDV", "down_seq": "PSPYSSSSWRRSRSPYSPVL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "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": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Ser383" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14004-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14004-1.369.369", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14004-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.395.395", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14004-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14004-1.400.400", "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": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.395.395", "start_pos": 395, "end_pos": 395, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SYERGGDVSPSPYSSSSWRR", "down_seq": "RSPYSPVLRRSGKSRSRSPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser395" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.383.383", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14004-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14004-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14004-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14004-1.400.400", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14004-1.411.411", "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": "Q14004-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ERGGDVSPSPYSSSSWRRSR", "down_seq": "PYSPVLRRSGKSRSRSPYSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser397" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14004-1.383.383", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14004-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.395.395", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14004-1.400.400", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.411.411", "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": "Q14004-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GGDVSPSPYSSSSWRRSRSP", "down_seq": "SPVLRRSGKSRSRSPYSSRH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Tyr399" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q14004-1.383.383", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14004-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14004-1.395.395", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14004-1.400.400", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.411.411", "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": "Q14004-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GDVSPSPYSSSSWRRSRSPY", "down_seq": "PVLRRSGKSRSRSPYSSRHS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser400" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14004-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q14004-1.383.383", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14004-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14004-1.395.395", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14004-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14004-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.411.411", "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": "Q14004-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "SRSPYSSRHSRSRSRHRLSR", "down_seq": "RSRHSSISPSTLTLKSSLAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser431" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14004-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14004-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14004-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.437.437", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14004-1.444.444", "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": "Q14004-1.437.437", "start_pos": 437, "end_pos": 437, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry.", "journal": "Anal. Chem.", "date": "2004", "authors": "Brill LM, Salomon AR, Ficarro SB, Mukherji M, Stettler-Gill M, Peters EC", "evidence": [ { "database": "UniProtKB", "id": "A0A2R8Y4Z0", "url": "https://www.uniprot.org/uniprotkb/A0A2R8Y4Z0" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "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": "SRHSRSRSRHRLSRSRSRHS", "down_seq": "ISPSTLTLKSSLAAELNKNK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser437" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q14004-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14004-1.431.431", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14004-1.444.444", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14004-1.456.456", "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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.439.439", "start_pos": 439, "end_pos": 439, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HSRSRSRHRLSRSRSRHSSI", "down_seq": "PSTLTLKSSLAAELNKNKKA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser439" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q14004-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14004-1.431.431", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14004-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.437.437", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14004-1.444.444", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14004-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14004-1.458.458", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.441.441", "start_pos": 441, "end_pos": 441, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Anal. Chem.", "date": "2004", "authors": "Brill LM, Salomon AR, Ficarro SB, Mukherji M, Stettler-Gill M, Peters EC", "evidence": [ { "database": "UniProtKB", "id": "A0A2R8Y4Z0", "url": "https://www.uniprot.org/uniprotkb/A0A2R8Y4Z0" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "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": "RSRSRHRLSRSRSRHSSISP", "down_seq": "TLTLKSSLAAELNKNKKARA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser441" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14004-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14004-1.431.431", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14004-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14004-1.437.437", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14004-1.444.444", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14004-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14004-1.458.458", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "IEDB", "id": "631102", "url": "https://www.iedb.org/epitope/631102" }, { "database": "IEDB", "id": "1356640", "url": "https://www.iedb.org/epitope/1356640" }, { "database": "IEDB", "id": "1366307", "url": "https://www.iedb.org/epitope/1366307" }, { "database": "IEDB", "id": "1370151", "url": "https://www.iedb.org/epitope/1370151" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "https://www.iedb.org/epitope/Q14004", "database": "IEDB", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SRSRHRLSRSRSRHSSISPS", "down_seq": "LTLKSSLAAELNKNKKARAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "IEDB", "id": "Q14004", "url": "https://www.iedb.org/epitope/Q14004" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Thr442" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14004-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14004-1.431.431", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14004-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14004-1.437.437", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.444.444", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14004-1.458.458", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14004-1.444.444", "start_pos": 444, "end_pos": 444, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "SRHRLSRSRSRHSSISPSTL", "down_seq": "LKSSLAAELNKNKKARAAEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Thr444" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14004-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14004-1.431.431", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14004-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14004-1.437.437", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14004-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14004-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14004-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14004-1.458.458", "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": "Q14004-1.493.493", "start_pos": 493, "end_pos": 493, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "journal": "Proteomics", "date": "2008", "authors": "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "evidence": [ { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAEATKAAEAAAKAAKASNT", "down_seq": "TPTKGNTETSASASQTNHVK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316" } ], "site_lbl": "Ser493" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q14004-1.490.490", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14004-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14004-1.505.505", "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": "Q14004-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AEATKAAEAAAKAAKASNTS", "down_seq": "PTKGNTETSASASQTNHVKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Thr494" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q14004-1.490.490", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14004-1.493.493", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14004-1.505.505", "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": "Q14004-1.525.525", "start_pos": 525, "end_pos": 525, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "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": "SASQTNHVKDVKKIKIEHAP", "down_seq": "PSSGGTLKNDKAKTKPPLQV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser525" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14004-1.505.505", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14004-1.527.527", "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": "Q14004-1.527.527", "start_pos": 527, "end_pos": 527, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "SQTNHVKDVKKIKIEHAPSP", "down_seq": "SGGTLKNDKAKTKPPLQVTK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser527" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q14004-1.525.525", "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": "Q14004-1.588.588", "start_pos": 588, "end_pos": 588, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SKSAATKEESVSLKEKTKPL", "down_seq": "PSIGAKEKEQHVALVTSTLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "site_lbl": "Thr588" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "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": "Q14004-1.624.624", "start_pos": 624, "end_pos": 624, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "TSTLPPLPLPPMLPEDKEAD", "down_seq": "LRGNISVKAVKKEVEKKLRC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser624" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "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": "Q14004-1.662.662", "start_pos": 662, "end_pos": 662, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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": "LRCLLADLPLPPELPGGDDL", "down_seq": "KSPEEKKTATQLHSKRRPKI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser662" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q14004-1.664.664", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14004-1.668.668", "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": "Q14004-1.664.664", "start_pos": 664, "end_pos": 664, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CLLADLPLPPELPGGDDLSK", "down_seq": "PEEKKTATQLHSKRRPKICG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser664" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q14004-1.662.662", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14004-1.668.668", "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": "Q14004-1.870.870", "start_pos": 870, "end_pos": 870, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "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" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QIKLADFGLARLYSSEESRP", "down_seq": "TNKVITLWYRPPELLLGEER", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr870" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q14004-1.871.871", "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": "Q14004-1.871.871", "start_pos": 871, "end_pos": 871, "uniprot_canonical_ac": "Q14004-1", "length": 1512, "uniprot_id": "CDK13_HUMAN", "protein_name": "Cyclin-dependent kinase 13", "refseq_ac": "NP_003709", "refseq_name": "cyclin-dependent kinase 13 isoform 1", "gene_name": "CDK13", "gene_names_uniprotkb": "CDK13; CDC2L5; CDC2L; CHED; KIAA1791", "gene_names_refseq": "CDC2L5; CDC2L; CDK13; CHDFIDD; CHED; hCDK13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "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": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "iPTMnet", "id": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q14004-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004", "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004", "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" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IKLADFGLARLYSSEESRPY", "down_seq": "NKVITLWYRPPELLLGEERY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q14004", "url": "https://www.uniprot.org/uniprotkb/Q14004" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q14004", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14004" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Thr871" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "1491", "end_pos": "1491" }, { "start_pos": "490", "end_pos": "490" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1000", "end_pos": "1000" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1153", "end_pos": "1153" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1286", "end_pos": "1286" }, { "start_pos": "1287", "end_pos": "1287" }, { "start_pos": "1288", "end_pos": "1288" }, { "start_pos": "1289", "end_pos": "1289" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1331", "end_pos": "1331" }, { "start_pos": "1354", "end_pos": "1354" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "566", "end_pos": "566" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "792", "end_pos": "792" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1146", "end_pos": "1146" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1471", "end_pos": "1471" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "871", "end_pos": "871" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q14004-1.870.870", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VVM6-1.372.372", "start_pos": 372, "end_pos": 372, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q5VVM6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VVM6" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VVM6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VVM6" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] } ], "crossref": [ { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VVM6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VVM6", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1271736726", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1271736726", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1271736726", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1271736726", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AEEKILDLQRKLEHAHKVCL", "down_seq": "DTCISEKQQLEEKIKEATQN", "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": "Thr372", "evidence": [ { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "Q5VVM6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VVM6" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" } ] } ], "snv": [ { "evidence": [ { "id": "rs1271736726", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1271736726" }, { "id": "rs1271736726", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1271736726" } ], "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": "42577149", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T372", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q5VVM6-1.368.368", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VVM6-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MSQEKNEMFESEWSK", "down_seq": "REREKQLASGLDTAEKALKV", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "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 (3).", "chr_id": "1", "chr_pos": "42536530", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E16", "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": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "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": "Q5VVM6-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "QQLHQNLHRLQILCNSAENE", "down_seq": "RYERGQNLDLKQHNSLLQEE", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "42566404", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L262", "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": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q5VVM6-1.263.263", "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": "Q5VVM6-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QLHQNLHRLQILCNSAENEL", "down_seq": "YERGQNLDLKQHNSLLQEEN", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "1", "chr_pos": "42566407", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R263", "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: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: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" ] }, { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "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 (4).", "chr_id": "1", "chr_pos": "42566408", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R263", "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" } ] }, { "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": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q5VVM6-1.262.262", "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": 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": "Q5VVM6-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759628119", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759628119", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759628119", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759628119", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759628119", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759628119", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HAQQKLLDSTKMCSSLTAEY", "down_seq": "HCQQKIKELELEVLKHTQSI", "snv": [ { "evidence": [ { "id": "rs759628119", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759628119" }, { "id": "rs759628119", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759628119" }, { "id": "rs759628119", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759628119" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KHC->NHC).", "chr_id": "1", "chr_pos": "42581449", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K312", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "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": "Q5VVM6-1.368.368", "start_pos": 368, "end_pos": 368, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KVADAEEKILDLQRKLEHAH", "down_seq": "VCLTDTCISEKQQLEEKIKE", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KVC->NVC).", "chr_id": "1", "chr_pos": "42581398", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K368", "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": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q5VVM6-1.372.372", "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": "Q5VVM6-1.415.415", "start_pos": 415, "end_pos": 415, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KVKQQYQEEQQKRKLLYQNV", "down_seq": "ELHRQVRTLQDKENLLEMTC", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "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": "1", "chr_pos": "42589343", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D415", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "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": "Q5VVM6-1.472.472", "start_pos": 472, "end_pos": 472, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1046091945", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1046091945", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1046091945", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1046091945#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1046091945", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1046091945", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LENEKRKYDEHVKSNQELSE", "down_seq": "LSKLQQEKEALREEYLRLLK", "snv": [ { "evidence": [ { "id": "rs1046091945", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1046091945" }, { "id": "rs1046091945", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1046091945#frequency_tab" }, { "id": "rs1046091945", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1046091945" } ], "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": "1", "chr_pos": "42577115", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K472", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "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": "Q5VVM6-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EELQKSKSELICLYNEVHNL", "down_seq": "GESESKDHFLIACDLLQREN", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLP->NLS).", "chr_id": "1", "chr_pos": "42539230", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P59", "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": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "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": "Q5VVM6-1.619.619", "start_pos": 619, "end_pos": 619, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ENKQLQENSLRLTQQIGFLE", "down_seq": "IIRSIHIRRGENLKEFPVPK", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "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 (3).", "chr_id": "1", "chr_pos": "42644773", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R619", "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: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": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "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": "Q5VVM6-1.714.714", "start_pos": 714, "end_pos": 714, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TISDILESEVVNEILPLSNS", "down_seq": "FSGKGLVESFASLQETEEIK", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "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 (SFS->NFS).", "chr_id": "1", "chr_pos": "42653443", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S714", "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": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "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": "Q5VVM6-1.766.766", "start_pos": 766, "end_pos": 766, "uniprot_canonical_ac": "Q5VVM6-1", "length": 783, "uniprot_id": "CCD30_HUMAN", "protein_name": "Coiled-coil domain-containing protein 30", "refseq_ac": "NP_001074319", "refseq_name": "coiled-coil domain-containing protein 30 isoform 1", "gene_name": "CCDC30", "gene_names_uniprotkb": "CCDC30; PFDN6L", "gene_names_refseq": "CCDC30; PFD6L; PFDN6L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVM6", "url": "https://www.uniprot.org/uniprotkb/Q5VVM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VVM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EKSPENLVCSQNSEAGYINV", "down_seq": "SLKETHGIQEQDQKSEL", "snv": [ { "evidence": [ { "id": "Q5VVM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VVM6" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVA->NVT).", "chr_id": "1", "chr_pos": "42653972", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A766", "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": "372", "end_pos": "372" } ] }, { "type": "snv", "site_list": [ { "start_pos": "16", "end_pos": "16" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "766", "end_pos": "766" } ] } ], "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": "Q6F5E8-1.1115.1115", "start_pos": 1115, "end_pos": 1115, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "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": "Q6F5E8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6F5E8" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q6F5E8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6F5E8" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6F5E8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6F5E8" }, { "database": "O-GlcNAc Atlas", "id": "Q6F5E8", "url": "https://oglcnac.org/atlas/detail/Q6F5E8" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Epigenetic co-regulator HCF-1 promotes lung cancer via O-GlcNAcylation-dependent pathways.", "journal": "Molecular therapy. Oncology", "date": "2025-12-18", "authors": "Srivastava Priyanka P, Dasari Abhilash, Kumar Saran, Gupta Ishaan, Jain Deepali, Minocha Shilpi", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6F5E8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6F5E8" } ], "reference": [ { "type": "PubMed", "id": "41018975", "url": "https://glygen.org/publication/PubMed/41018975" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6F5E8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6F5E8", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "41018975", "url": "https://glygen.org/publication/PubMed/41018975", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6F5E8", "url": "https://oglcnac.org/atlas/detail/Q6F5E8", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RKKLGTLFAFKKPRSTRGPR", "down_seq": "DLETSPGAAPRTRKTTFGDL", "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": "Thr1115", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "Q6F5E8", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6F5E8" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "41018975", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/41018975" }, { "id": "Q6F5E8", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6F5E8" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6F5E8-1.1095.1095", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6F5E8-1.1096.1106", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6F5E8-1.1120.1120", "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": 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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6F5E8-1.1412.1412", "start_pos": 1412, "end_pos": 1412, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "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": "APPSPSLGSGLGTEPLPPQP", "down_seq": "EPSSPERSPPSPATDQRGGG", "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": "Thr1412", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q6F5E8-1.1420.1420", "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": "Q6F5E8-1.647.647", "start_pos": 647, "end_pos": 647, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KLLAKALRVNSRLRSVVWDR", "down_seq": "HTSALGLLDVAQALEQNHSL", "glycosylation": [ { "glytoucan_ac": "G22784RF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NHTSALGLLDVAQALEQNHSLKAMPLPLNDVAQAQRSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn647", "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.649.649", "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": 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": 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": "Q6F5E8-1.1021.1021", "start_pos": 1021, "end_pos": 1021, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "CARMIL2 is a novel molecular connection between vimentin and actin essential for cell migration and invadopodia formation.", "journal": "Molecular biology of the cell", "date": "2015", "authors": "Lanier MH, Kim T, Cooper JA", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "RefSeq", "id": "NP_001013860", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001013860" } ], "reference": [ { "type": "PubMed", "id": "26466680", "url": "https://glygen.org/publication/PubMed/26466680" } ] } ], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26466680", "url": "https://glygen.org/publication/PubMed/26466680", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AGPLPRMDLPLAGQPLRHPT", "down_seq": "ARPRPRRQHHHRPPPGGPQV", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Loss of ability to bind heterodimeric capping protein (CP), unable to inhibit the actin-capping activity of CP and to rescue the loss of lamellipodial ruffling, macropinocytosis, cell polarity, and invadopodia-mediated matrix degradation; when associated with A-1023.", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "PubMed", "id": "26466680", "url": "https://glygen.org/publication/PubMed/26466680" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q6F5E8-1.1023.1023", "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": "Q6F5E8-1.1023.1023", "start_pos": 1023, "end_pos": 1023, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "CARMIL2 is a novel molecular connection between vimentin and actin essential for cell migration and invadopodia formation.", "journal": "Molecular biology of the cell", "date": "2015", "authors": "Lanier MH, Kim T, Cooper JA", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "RefSeq", "id": "NP_001013860", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001013860" } ], "reference": [ { "type": "PubMed", "id": "26466680", "url": "https://glygen.org/publication/PubMed/26466680" } ] } ], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26466680", "url": "https://glygen.org/publication/PubMed/26466680", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PLPRMDLPLAGQPLRHPTRA", "down_seq": "PRPRRQHHHRPPPGGPQVPP", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Loss of ability to bind heterodimeric capping protein (CP), unable to inhibit the actin-capping activity of CP and to rescue the loss of lamellipodial ruffling, macropinocytosis, cell polarity, and invadopodia-mediated matrix degradation; when associated with A-1021.", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "PubMed", "id": "26466680", "url": "https://glygen.org/publication/PubMed/26466680" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6F5E8-1.1021.1021", "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": "Q6F5E8-1.1096.1106", "start_pos": 1096, "end_pos": 1106, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cell Migration and Invadopodia Formation Require a Membrane-binding Domain of CARMIL2.", "journal": "The Journal of biological chemistry", "date": "2016", "authors": "Lanier MH, McConnell P, Cooper JA", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "RefSeq", "id": "NP_001013860", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001013860" } ], "reference": [ { "type": "PubMed", "id": "26578515", "url": "https://glygen.org/publication/PubMed/26578515" } ] } ], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26578515", "url": "https://glygen.org/publication/PubMed/26578515", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "KKLGTLFAFKK", "start_aa": "K", "up_seq": "APEEDPATEGGATPVPRTLR", "down_seq": "PRSTRGPRTDLETSPGAAPR", "mutagenesis": [ { "sequence_org": "KKLGTLFAFKK", "sequence_mut": "EEEEEEEEEEE", "comment": "Loss of accumulation at the cell membrane. Does not alter colocalization at vimentin filaments. Alters monopolar cell polarity, increasing the number of leading edges lacking lamellipodia and ruffles. Inhibits cell migration during wound healing.", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "PubMed", "id": "26578515", "url": "https://glygen.org/publication/PubMed/26578515" } ] }, { "sequence_org": "KKLGTLFAFKK", "sequence_mut": "GGGGGGGGGGG", "comment": "Loss of accumulation at the cell membrane. Does not alter colocalization at vimentin filaments. Alters monopolar cell polarity, increasing the number of leading edges lacking lamellipodia and ruffles. Inhibits cell migration during wound healing.", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "PubMed", "id": "26578515", "url": "https://glygen.org/publication/PubMed/26578515" } ] }, { "sequence_org": "KKLGTLFAFKK", "sequence_mut": "", "comment": "Loss of accumulation at the cell membrane. Does not alter colocalization at vimentin filaments. Alters monopolar cell polarity, increasing the number of leading edges lacking lamellipodia and ruffles. Inhibits cell migration during wound healing.", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "PubMed", "id": "26578515", "url": "https://glygen.org/publication/PubMed/26578515" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6F5E8-1.1082.1082", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6F5E8-1.1095.1095", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6F5E8-1.1115.1115", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6F5E8-1.1120.1120", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6F5E8-1.1082.1082", "start_pos": 1082, "end_pos": 1082, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EFFSKRLIQQDRLWAPEEDP", "down_seq": "TEGGATPVPRTLRKKLGTLF", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" } ], "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": "16", "chr_pos": "67654355", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1082", "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": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.1095.1095", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6F5E8-1.1096.1106", "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": "Q6F5E8-1.1095.1095", "start_pos": 1095, "end_pos": 1095, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WAPEEDPATEGGATPVPRTL", "down_seq": "KKLGTLFAFKKPRSTRGPRT", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "67654394", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1095", "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: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": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.1082.1082", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6F5E8-1.1096.1106", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6F5E8-1.1115.1115", "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": "Q6F5E8-1.1230.1230", "start_pos": 1230, "end_pos": 1230, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "EQRVQVMLQRIGVSRGSGGA", "down_seq": "GKRKQSKDGEIKKAGSDGDI", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "67654883", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E1230", "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: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": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q6F5E8-1.1246.1246", "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": "Q6F5E8-1.1253.1253", "start_pos": 1253, "end_pos": 1253, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1309768374", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309768374", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1309768374", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309768374#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1309768374", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309768374", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKQSKDGEIKKAGSDGDIMD", "down_seq": "STEAPPISIKSRTHSVSADP", "snv": [ { "evidence": [ { "id": "rs1309768374", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309768374" }, { "id": "rs1309768374", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309768374#frequency_tab" }, { "id": "rs1309768374", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309768374" } ], "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": "16", "chr_pos": "67656243", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1253", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.1246.1246", "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": "Q6F5E8-1.1374.1374", "start_pos": 1374, "end_pos": 1374, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LSAGRRAVSVHEDQLQAPAE", "down_seq": "PLRLQRSPVLKRRPKLEAPP", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "67657242", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1374", "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: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": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KLFRRPTPASMLARLERSSP", "down_seq": "ESTDPCSPCGGFLETYEALC", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" } ], "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": "16", "chr_pos": "67646488", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S146", "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: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": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.174.174", "start_pos": 174, "end_pos": 174, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PCGGFLETYEALCDYNGFPF", "down_seq": "EEIQWDVDTIYHRQGCRHFS", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "67646767", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R174", "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" } ] }, { "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": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759719206", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759719206", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759719206", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759719206", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759719206", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759719206", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IQWDVDTIYHRQGCRHFSLG", "down_seq": "FSHLGSRDLALSVAALSYNL", "snv": [ { "evidence": [ { "id": "rs759719206", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759719206" }, { "id": "rs759719206", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759719206" }, { "id": "rs759719206", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759719206" } ], "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": "16", "chr_pos": "67646951", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D197", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1567627646", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567627646", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1567627646", "url": "https://www.ensembl.org/id/rs1567627646", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSCVDMKLSLEVSEQILHMM", "down_seq": "QSSHLEELVLETCSLRGDFV", "snv": [ { "evidence": [ { "id": "rs1567627646", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567627646" }, { "id": "rs1567627646", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1567627646" } ], "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 (SQS->NQS).", "chr_id": "16", "chr_pos": "67647336", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S242", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q6F5E8-1.254.254", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6F5E8-1.254.254", "start_pos": 254, "end_pos": 254, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751283384", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751283384", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751283384", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751283384", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751283384", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751283384", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SEQILHMMSQSSHLEELVLE", "down_seq": "CSLRGDFVRRLAQALAGHSS", "snv": [ { "evidence": [ { "id": "rs751283384", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751283384" }, { "id": "rs751283384", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751283384" }, { "id": "rs751283384", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751283384" } ], "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 (TCS->NCS).", "chr_id": "16", "chr_pos": "67647372", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T254", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.242.242", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6F5E8-1.333.333", "start_pos": 333, "end_pos": 333, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs772486345", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772486345", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772486345", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772486345", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772486345", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772486345#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772486345", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772486345", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QTGLTPRGMRALGRALATNA", "down_seq": "FDSTLTHLDLSGNPGALGAS", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" }, { "id": "rs772486345", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772486345" }, { "id": "rs772486345", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772486345" }, { "id": "rs772486345", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772486345#frequency_tab" }, { "id": "rs772486345", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772486345" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAA->NAT).", "chr_id": "16", "chr_pos": "67647884", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A333", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.335.335", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6F5E8-1.335.335", "start_pos": 335, "end_pos": 335, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760848421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760848421", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760848421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760848421", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760848421", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760848421", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs760848421", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760848421", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GLTPRGMRALGRALATNAAF", "down_seq": "STLTHLDLSGNPGALGASED", "snv": [ { "evidence": [ { "id": "rs760848421", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760848421" }, { "id": "rs760848421", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760848421" }, { "id": "rs760848421", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760848421" }, { "id": "rs760848421", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760848421" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DST->NST).", "chr_id": "NC_000016.10", "chr_pos": "67647890", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "0.000004797", "site_lbl": "D335", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.333.333", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6F5E8-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs898513011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs898513011", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs898513011", "url": "https://www.ncbi.nlm.nih.gov/snp/rs898513011#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs898513011", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs898513011", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs898513011", "url": "http://gnomad.broadinstitute.org/awesome?query=rs898513011", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DSGGLYSFLSRPNVLSFLNL", "down_seq": "GTDTALDTVRGCSVGGWMTG", "snv": [ { "evidence": [ { "id": "rs898513011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs898513011" }, { "id": "rs898513011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs898513011#frequency_tab" }, { "id": "rs898513011", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs898513011" }, { "id": "rs898513011", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs898513011" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLT).", "chr_id": "NC_000016.10", "chr_pos": "67648103", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "0.000010", "site_lbl": "A375", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.436.436", "start_pos": 436, "end_pos": 436, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1435568240", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435568240", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1435568240", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435568240", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LPPQLFAAVSRGCCTSLTHL", "down_seq": "ASRNVFSRTKSRAAPAALQL", "snv": [ { "evidence": [ { "id": "rs1435568240", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435568240" }, { "id": "rs1435568240", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435568240" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DAS->NAS).", "chr_id": "16", "chr_pos": "67648286", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D436", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.498.498", "start_pos": 498, "end_pos": 498, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758570868", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758570868", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758570868", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758570868", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758570868", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758570868#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758570868", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758570868", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ALRALLDGLALNTHLRDLHL", "down_seq": "LSACELRSAGAQVIQDLVCD", "snv": [ { "evidence": [ { "id": "rs758570868", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758570868" }, { "id": "rs758570868", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758570868" }, { "id": "rs758570868", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758570868#frequency_tab" }, { "id": "rs758570868", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758570868" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "16", "chr_pos": "67648737", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D498", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.580.580", "start_pos": 580, "end_pos": 580, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2543552546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2543552546", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VRCKETLDDVLHRIVQLMQD", "down_seq": "DCPLQSLSVAESRLKLGASV", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" }, { "id": "rs2543552546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2543552546" } ], "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 (DDC->NDC).", "chr_id": "16", "chr_pos": "67649303", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D580", "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": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.649.649", "start_pos": 649, "end_pos": 649, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2052686186", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2052686186", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2052686186", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2052686186#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LAKALRVNSRLRSVVWDRNH", "down_seq": "SALGLLDVAQALEQNHSLKA", "snv": [ { "evidence": [ { "id": "rs2052686186", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2052686186" }, { "id": "rs2052686186", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2052686186#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 (NHT->NHA).", "chr_id": "16", "chr_pos": "67649831", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T649", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.647.647", "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": "Q6F5E8-1.704.704", "start_pos": 704, "end_pos": 704, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752548336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752548336", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752548336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752548336", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752548336", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752548336#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752548336", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752548336", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs752548336", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs752548336", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RPELTARAVHQIQACLLRNN", "down_seq": "ADPASSDHTTRLQPLGLVSD", "snv": [ { "evidence": [ { "id": "rs752548336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752548336" }, { "id": "rs752548336", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752548336" }, { "id": "rs752548336", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752548336#frequency_tab" }, { "id": "rs752548336", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752548336" }, { "id": "rs752548336", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs752548336" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNR->NNC).", "chr_id": "16", "chr_pos": "67650076", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R704", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.705.705", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6F5E8-1.705.705", "start_pos": 705, "end_pos": 705, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs748613858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748613858", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748613858", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748613858#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748613858", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748613858", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PELTARAVHQIQACLLRNNR", "down_seq": "DPASSDHTTRLQPLGLVSDP", "snv": [ { "evidence": [ { "id": "Q6F5E8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6F5E8" }, { "id": "rs748613858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748613858" }, { "id": "rs748613858", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748613858#frequency_tab" }, { "id": "rs748613858", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748613858" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRA->NRT).", "chr_id": "16", "chr_pos": "67650079", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A705", "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": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.704.704", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6F5E8-1.767.767", "start_pos": 767, "end_pos": 767, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs985801648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs985801648", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs985801648", "url": "https://www.ensembl.org/id/rs985801648", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GAGPQGEAAVRQAEDAIQNA", "down_seq": "FSLSILPILYEAGSSPSHHW", "snv": [ { "evidence": [ { "id": "rs985801648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs985801648" }, { "id": "rs985801648", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs985801648" } ], "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 (NAN->NAS).", "chr_id": "16", "chr_pos": "67651302", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N767", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "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": "Q6F5E8-1.1120.1120", "start_pos": 1120, "end_pos": 1120, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLFAFKKPRSTRGPRTDLET", "down_seq": "PGAAPRTRKTTFGDLLRPPT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "site_lbl": "Ser1120" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6F5E8-1.1096.1106", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6F5E8-1.1115.1115", "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": "Q6F5E8-1.1246.1246", "start_pos": 1246, "end_pos": 1246, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "iPTMnet", "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q6F5E8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8", "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": "SGGAEGKRKQSKDGEIKKAG", "down_seq": "DGDIMDSSTEAPPISIKSRT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser1246" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6F5E8-1.1230.1230", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6F5E8-1.1253.1253", "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": "Q6F5E8-1.1315.1315", "start_pos": 1315, "end_pos": 1315, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLNAELRSRGWGQQDGPGPP", "down_seq": "PGQSPSPCRTSPSPDSLGLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "site_lbl": "Ser1315" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "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": "Q6F5E8-1.1420.1420", "start_pos": 1420, "end_pos": 1420, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGLGTEPLPPQPTEPSSPER", "down_seq": "PPSPATDQRGGGPNP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "site_lbl": "Ser1420" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6F5E8-1.1412.1412", "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": "Q6F5E8-1.991.991", "start_pos": 991, "end_pos": 991, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "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": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "iPTMnet", "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "iPTMnet", "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q6F5E8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8", "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": "PELAAPGEDAEPQAGPSARG", "down_seq": "PSPAAPGPPAGPLPRMDLPL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser991" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q6F5E8-1.993.993", "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": "Q6F5E8-1.993.993", "start_pos": 993, "end_pos": 993, "uniprot_canonical_ac": "Q6F5E8-1", "length": 1435, "uniprot_id": "CARL2_HUMAN", "protein_name": "Capping protein, Arp2/3 and myosin-I linker protein 2", "refseq_ac": "NP_001013860", "refseq_name": "capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1", "gene_name": "CARMIL2", "gene_names_uniprotkb": "CARMIL2; LRRC16C; RLTPR", "gene_names_refseq": "CARMIL2b; CARMIL2; IMD58; LRRC16C; RLTPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "iPTMnet", "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q6F5E8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] } ], "crossref": [ { "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8", "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": "LAAPGEDAEPQAGPSARGSP", "down_seq": "PAAPGPPAGPLPRMDLPLAG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6F5E8", "url": "https://www.uniprot.org/uniprotkb/Q6F5E8" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "Q6F5E8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6F5E8" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Ser993" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1412", "end_pos": "1412" }, { "start_pos": "647", "end_pos": "647" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1023", "end_pos": "1023" }, { "start_pos": "1096", "end_pos": "1106" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1230", "end_pos": "1230" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "1374", "end_pos": "1374" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "767", "end_pos": "767" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1120", "end_pos": "1120" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6F5E8-1.991.991", "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": "Q15777-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "Q15777-1", "length": 294, "uniprot_id": "MPPD2_HUMAN", "protein_name": "Metallophosphoesterase MPPED2", "refseq_ac": "NP_001138871", "refseq_name": "metallophosphoesterase MPPED2 isoform 2", "gene_name": "MPPED2", "gene_names_uniprotkb": "MPPED2; C11orf8; FAM1B", "gene_names_refseq": "239FB; C11orf8; MPPED2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15777", "url": "https://www.uniprot.org/uniprotkb/Q15777" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15777", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "FMADLVKQDYYRFPSVSKLK", "down_seq": "EDFDNVQSLLTNSIYLQDSE", "snv": [ { "evidence": [ { "id": "Q15777", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "30495396", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P146", "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": "146", "end_pos": "146" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "245", "end_pos": "245" } ] } ], "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": "Q15777-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "Q15777-1", "length": 294, "uniprot_id": "MPPD2_HUMAN", "protein_name": "Metallophosphoesterase MPPED2", "refseq_ac": "NP_001138871", "refseq_name": "metallophosphoesterase MPPED2 isoform 2", "gene_name": "MPPED2", "gene_names_uniprotkb": "MPPED2; C11orf8; FAM1B", "gene_names_refseq": "239FB; C11orf8; MPPED2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15777", "url": "https://www.uniprot.org/uniprotkb/Q15777" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15777", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MAHGIPSQGKVTI", "down_seq": "VDEYSSNPTQAFTHYNINQS", "snv": [ { "evidence": [ { "id": "Q15777", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "30580333", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T14", "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": "146", "end_pos": "146" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "245", "end_pos": "245" } ] } ], "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": "Q15777-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "Q15777-1", "length": 294, "uniprot_id": "MPPD2_HUMAN", "protein_name": "Metallophosphoesterase MPPED2", "refseq_ac": "NP_001138871", "refseq_name": "metallophosphoesterase MPPED2 isoform 2", "gene_name": "MPPED2", "gene_names_uniprotkb": "MPPED2; C11orf8; FAM1B", "gene_names_refseq": "239FB; C11orf8; MPPED2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15777", "url": "https://www.uniprot.org/uniprotkb/Q15777" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15777", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LTNSIYLQDSEVTVKGFRIY", "down_seq": "APWTPWFNGWGFNLPRGQSL", "snv": [ { "evidence": [ { "id": "Q15777", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "30495306", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G176", "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: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": "146", "end_pos": "146" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "245", "end_pos": "245" } ] } ], "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": "Q15777-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "Q15777-1", "length": 294, "uniprot_id": "MPPD2_HUMAN", "protein_name": "Metallophosphoesterase MPPED2", "refseq_ac": "NP_001138871", "refseq_name": "metallophosphoesterase MPPED2 isoform 2", "gene_name": "MPPED2", "gene_names_uniprotkb": "MPPED2; C11orf8; FAM1B", "gene_names_refseq": "239FB; C11orf8; MPPED2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15777", "url": "https://www.uniprot.org/uniprotkb/Q15777" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15777", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "WGFNLPRGQSLLDKWNLIPE", "down_seq": "IDILMTHGPPLGFRDWVPKE", "snv": [ { "evidence": [ { "id": "Q15777", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777" } ], "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": "11", "chr_pos": "30417554", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G206", "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": "146", "end_pos": "146" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q15777-1.220.220", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15777-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "Q15777-1", "length": 294, "uniprot_id": "MPPD2_HUMAN", "protein_name": "Metallophosphoesterase MPPED2", "refseq_ac": "NP_001138871", "refseq_name": "metallophosphoesterase MPPED2 isoform 2", "gene_name": "MPPED2", "gene_names_uniprotkb": "MPPED2; C11orf8; FAM1B", "gene_names_refseq": "239FB; C11orf8; MPPED2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15777", "url": "https://www.uniprot.org/uniprotkb/Q15777" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15777", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WNLIPEGIDILMTHGPPLGF", "down_seq": "DWVPKELQRVGCVELLNTVQ", "snv": [ { "evidence": [ { "id": "Q15777", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "30414336", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R220", "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: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": "146", "end_pos": "146" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q15777-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q15777-1.238.238", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15777-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "Q15777-1", "length": 294, "uniprot_id": "MPPD2_HUMAN", "protein_name": "Metallophosphoesterase MPPED2", "refseq_ac": "NP_001138871", "refseq_name": "metallophosphoesterase MPPED2 isoform 2", "gene_name": "MPPED2", "gene_names_uniprotkb": "MPPED2; C11orf8; FAM1B", "gene_names_refseq": "239FB; C11orf8; MPPED2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15777", "url": "https://www.uniprot.org/uniprotkb/Q15777" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15777", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GFRDWVPKELQRVGCVELLN", "down_seq": "VQRRVRPKLHVFGGIHEGYG", "snv": [ { "evidence": [ { "id": "Q15777", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777" } ], "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": "11", "chr_pos": "30414281", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T238", "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": "146", "end_pos": "146" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q15777-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q15777-1.245.245", "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": "Q15777-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "Q15777-1", "length": 294, "uniprot_id": "MPPD2_HUMAN", "protein_name": "Metallophosphoesterase MPPED2", "refseq_ac": "NP_001138871", "refseq_name": "metallophosphoesterase MPPED2 isoform 2", "gene_name": "MPPED2", "gene_names_uniprotkb": "MPPED2; C11orf8; FAM1B", "gene_names_refseq": "239FB; C11orf8; MPPED2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15777", "url": "https://www.uniprot.org/uniprotkb/Q15777" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15777", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KELQRVGCVELLNTVQRRVR", "down_seq": "KLHVFGGIHEGYGIMTDGYT", "snv": [ { "evidence": [ { "id": "Q15777", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15777" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "11", "chr_pos": "30414260", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P245", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q15777-1.238.238", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "P43403-1.497.497", "start_pos": 497, "end_pos": 497, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "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": "P43403", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P43403" }, { "database": "O-GlcNAc Atlas", "id": "P43403", "url": "https://oglcnac.org/atlas/detail/P43403" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P43403", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P43403" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P43403", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "https://oglcnac.org/atlas/detail/P43403", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs149765220", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149765220", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149765220", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149765220", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs149765220", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149765220", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs149765220", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149765220#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs149765220", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149765220", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1677963080", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1677963080", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1677963080", "url": "https://www.ensembl.org/id/rs1677963080", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ISDFGLSKALGADDSYYTAR", "down_seq": "AGKWPLKWYAPECINFRKFS", "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": "Ser497", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "P43403", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P43403" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "P43403", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P43403" } ] } ], "snv": [ { "evidence": [ { "id": "rs149765220", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149765220" }, { "id": "rs149765220", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149765220" }, { "id": "rs149765220", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149765220" }, { "id": "rs149765220", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149765220#frequency_tab" }, { "id": "rs149765220", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149765220" } ], "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": "2", "chr_pos": "97737764", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S497", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1677963080", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1677963080" }, { "id": "rs1677963080", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1677963080" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "2", "chr_pos": "97737763", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S497", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43403-1.479.479", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43403-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43403-1.492.492", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43403-1.493.493", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43403-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43403-1.514.514", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.131.131", "start_pos": 131, "end_pos": 131, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "QPGVFDCLRDAMVRDYVRQT", "down_seq": "KLEGEALEQAIISQAPQVEK", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "A", "comment": "Increased constitutive kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P43403-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43403-1.126.126", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43403-1.133.133", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43403-1.141.141", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43403-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43403-1.145.145", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43403-1.147.147", "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": "P43403-1.133.133", "start_pos": 133, "end_pos": 133, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GVFDCLRDAMVRDYVRQTWK", "down_seq": "EGEALEQAIISQAPQVEKLI", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "Increased constitutive kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P43403-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43403-1.126.126", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43403-1.131.131", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43403-1.141.141", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43403-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43403-1.145.145", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43403-1.147.147", "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": "P43403-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AMVRDYVRQTWKLEGEALEQ", "down_seq": "IISQAPQVEKLIATTAHERM", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "E", "comment": "Increased constitutive kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P43403-1.126.126", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43403-1.131.131", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43403-1.133.133", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43403-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43403-1.145.145", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43403-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43403-1.159.159", "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": "P43403-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RDYVRQTWKLEGEALEQAII", "down_seq": "QAPQVEKLIATTAHERMPWY", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Increased kinase activity after activation by LCK.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43403-1.126.126", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43403-1.131.131", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43403-1.133.133", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43403-1.141.141", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.145.145", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43403-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43403-1.159.159", "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": "P43403-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "DYVRQTWKLEGEALEQAIIS", "down_seq": "APQVEKLIATTAHERMPWYH", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Increased kinase activity after activation by LCK.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43403-1.126.126", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43403-1.131.131", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43403-1.133.133", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43403-1.141.141", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43403-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43403-1.159.159", "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": "P43403-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VRQTWKLEGEALEQAIISQA", "down_seq": "QVEKLIATTAHERMPWYHSS", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "Increased kinase activity after activation by LCK.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P43403-1.131.131", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43403-1.133.133", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43403-1.141.141", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43403-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43403-1.145.145", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43403-1.159.159", "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": "P43403-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Chan AY, Punwani D, Kadlecek TA, Cowan MJ, Olson JL, Mathes EF, Sunderam U, Fu SM, Srinivasan R, Kuriyan J, Brenner SE, Weiss A, Puck JM", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "REEAERKLYSGAQTDGKFLL", "down_seq": "PRKEQGTYALSLIYGKTVYH", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "K", "comment": "Decreases interaction with phosphorylated CD247; when associated with K-37.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P43403-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.191.191", "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": "P43403-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Enhancement of lymphocyte responsiveness by a gain-of-function mutation of ZAP-70.", "journal": "Molecular and cellular biology", "date": "1996", "authors": "Zhao Q, Weiss A", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "8943331", "url": "https://glygen.org/publication/PubMed/8943331" } ] }, { "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": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] }, { "title": "Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2009", "authors": "St-Germain JR, Taylor P, Tong J, Jin LL, Nikolic A, Stewart II, Ewing RM, Dharsee M, Li Z, Trudel S, Moran MF", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" } ] }, { "title": "Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "Watts JD, Affolter M, Krebs DL, Wange RL, Samelson LE, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ] }, { "title": "Tyrosine 319, a newly identified phosphorylation site of ZAP-70, plays a critical role in T cell antigen receptor signaling.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Di Bartolo V, Mege D, Germain V, Pelosi M, Dufour E, Michel F, Magistrelli G, Isacchi A, Acuto O", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" } ] }, { "title": "Distinct tyrosine phosphorylation sites in ZAP-70 mediate activation and negative regulation of antigen receptor function.", "journal": "Molecular and cellular biology", "date": "1996", "authors": "Kong G, Dalton M, Bubeck Wardenburg J, Straus D, Kurosaki T, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "The linker phosphorylation site Tyr292 mediates the negative regulatory effect of Cbl on ZAP-70 in T cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2000", "authors": "Rao N, Lupher ML Jr, Ota S, Reedquist KA, Druker BJ, Band H", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "10779765", "url": "https://glygen.org/publication/PubMed/10779765" } ] }, { "title": "Intracellular Phospho-Flow cytometry reveals novel insights into TCR proximal signaling events. A comparison with Western blot.", "journal": "Cytometry. Part A : the journal of the International Society for Analytical Cytology", "date": "2008", "authors": "Haas A, Weckbecker G, Welzenbach K", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "18548611", "url": "https://glygen.org/publication/PubMed/18548611" } ] }, { "title": "ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells.", "journal": "PloS one", "date": "2013", "authors": "Helou YA, Nguyen V, Beik SP, Salomon AR", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" } ] }, { "title": "The function of a novel immunophenotype candidate molecule PD-1 in chronic lymphocytic leukemia.", "journal": "Leukemia & lymphoma", "date": "2015", "authors": "Grzywnowicz M, Karabon L, Karczmarczyk A, Zajac M, Skorka K, Zaleska J, Wlasiuk P, Chocholska S, Tomczak W, Bojarska-Junak A, Dmoszynska A, Frydecka I, Giannopoulos K", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "25682964", "url": "https://glygen.org/publication/PubMed/25682964" } ] }, { "title": "ZAP-70 protein tyrosine kinase is constitutively targeted to the T cell cortex independently of its SH2 domains.", "journal": "The Journal of cell biology", "date": "1997", "authors": "Huby RD, Iwashima M, Weiss A, Ley SC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177" } ] }, { "title": "The Cbl phosphotyrosine-binding domain selects a D(N/D)XpY motif and binds to the Tyr292 negative regulatory phosphorylation site of ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1997", "authors": "Lupher ML Jr, Songyang Z, Shoelson SE, Cantley LC, Band H", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "9407100", "url": "https://glygen.org/publication/PubMed/9407100" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8943331", "url": "https://glygen.org/publication/PubMed/8943331", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10779765", "url": "https://glygen.org/publication/PubMed/10779765", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18548611", "url": "https://glygen.org/publication/PubMed/18548611", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25682964", "url": "https://glygen.org/publication/PubMed/25682964", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9407100", "url": "https://glygen.org/publication/PubMed/9407100", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AHPSTLTHPQRRIDTLNSDG", "down_seq": "TPEPARITSPDKPRPMPMDT", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Induces constitutive TCR stimulation-independent NFAT induction.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "8943331", "url": "https://glygen.org/publication/PubMed/8943331" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P43403-1", "kinase_gene_name": "ZAP70", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" }, { "database": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" }, { "database": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ], "site_lbl": "Tyr292" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "8943331", "url": "https://glygen.org/publication/PubMed/8943331" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "10779765", "url": "https://glygen.org/publication/PubMed/10779765" }, { "database": "PubMed", "id": "18548611", "url": "https://glygen.org/publication/PubMed/18548611" }, { "database": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" }, { "database": "PubMed", "id": "25682964", "url": "https://glygen.org/publication/PubMed/25682964" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177" }, { "database": "PubMed", "id": "9407100", "url": "https://glygen.org/publication/PubMed/9407100" } ], "site_lbl": "Tyr292" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P43403-1.289.289", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.293.293", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43403-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43403-1.304.304", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Otud7b facilitates T cell activation and inflammatory responses by regulating Zap70 ubiquitination.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Hu H, Wang H, Xiao Y, Jin J, Chang JH, Zou Q, Xie X, Cheng X, Sun SC", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IDTLNSDGYTPEPARITSPD", "down_seq": "PRPMPMDTSVYESPYSDPEE", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "No effect on ubiquitination.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P43403-1.289.289", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43403-1.292.292", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43403-1.293.293", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43403-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43403-1.314.314", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43403-1.315.315", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43403-1.315.319", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43403-1.319.319", "categories": [ "mutagenesis_flag", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PEPARITSPDKPRPMPMDTS", "down_seq": "YESPYSDPEELKDKKLFLKR", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "A", "comment": "Increased constitutive kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P43403-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43403-1.304.304", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.315.315", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.315.319", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43403-1.319.319", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43403-1.327.327", "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": 0 } ], "sort_fields": [] } ] }, { "id": "P43403-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] }, { "title": "Tyrosine 319, a newly identified phosphorylation site of ZAP-70, plays a critical role in T cell antigen receptor signaling.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Di Bartolo V, Mege D, Germain V, Pelosi M, Dufour E, Michel F, Magistrelli G, Isacchi A, Acuto O", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" } ] }, { "title": "The Vav binding site (Y315) in ZAP-70 is critical for antigen receptor-mediated signal transduction.", "journal": "The Journal of experimental medicine", "date": "1997", "authors": "Wu J, Zhao Q, Kurosaki T, Weiss A", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "9151714", "url": "https://glygen.org/publication/PubMed/9151714" } ] }, { "title": "Tyrosine 315 determines optimal recruitment of ZAP-70 to the T cell antigen receptor.", "journal": "European journal of immunology", "date": "2002", "authors": "Di Bartolo V, Malissen M, Dufour E, Sechet E, Malissen B, Acuto O", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "11828374", "url": "https://glygen.org/publication/PubMed/11828374" } ] }, { "title": "Distinct tyrosine phosphorylation sites in ZAP-70 mediate activation and negative regulation of antigen receptor function.", "journal": "Molecular and cellular biology", "date": "1996", "authors": "Kong G, Dalton M, Bubeck Wardenburg J, Straus D, Kurosaki T, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ] }, { "title": "T cell activation-induced CrkII binding to the Zap70 protein tyrosine kinase is mediated by Lck-dependent phosphorylation of Zap70 tyrosine 315.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2005", "authors": "Gelkop S, Gish GD, Babichev Y, Pawson T, Isakov N", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "16339550", "url": "https://glygen.org/publication/PubMed/16339550" } ] }, { "title": "Requirement for tyrosine residues 315 and 319 within zeta chain-associated protein 70 for T cell development.", "journal": "The Journal of experimental medicine", "date": "2001", "authors": "Gong Q, Jin X, Akk AM, Foger N, White M, Gong G, Bubeck Wardenburg J, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606" } ] }, { "title": "MTOC translocation modulates IS formation and controls sustained T cell signaling.", "journal": "The Journal of cell biology", "date": "2008", "authors": "Martin-Cofreces NB, Robles-Valero J, Cabrero JR, Mittelbrunn M, Gordon-Alonso M, Sung CH, Alarcon B, Vazquez J, Sanchez-Madrid F", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "18779373", "url": "https://glygen.org/publication/PubMed/18779373" } ] }, { "title": "RhoH regulates subcellular localization of ZAP-70 and Lck in T cell receptor signaling.", "journal": "PloS one", "date": "2010", "authors": "Chae HD, Siefring JE, Hildeman DA, Gu Y, Williams DA", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055" } ] }, { "title": "Mathematical modeling identifies Lck as a potential mediator for PD-1 induced inhibition of early TCR signaling.", "journal": "PloS one", "date": "2018", "authors": "Arulraj T, Barik D", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330" } ] }, { "title": "CCR7 Is Recruited to the Immunological Synapse, Acts as Co-stimulatory Molecule and Drives LFA-1 Clustering for Efficient T Cell Adhesion Through ZAP70.", "journal": "Frontiers in immunology", "date": "2018", "authors": "Laufer JM, Kindinger I, Artinger M, Pauli A, Legler DF", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "30692994", "url": "https://glygen.org/publication/PubMed/30692994" } ] }, { "title": "CD103 Promotes the Pro-inflammatory Response of Gastric Resident CD4+ T Cell in Helicobacter pylori-Positive Gastritis.", "journal": "Frontiers in cellular and infection microbiology", "date": "2020", "authors": "Chen Peiyu, Ming Siqi, Lao Juanfeng, Li Chunna, Wang Hongli, Xiong Liya, Zhang Shunxian, Liang Zibin, Niu Xiaoli, Deng Simei, Geng Lanlan, Wu Minhao, Wu Yongjian, Gong Sitang", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "32974219", "url": "https://glygen.org/publication/PubMed/32974219" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9151714", "url": "https://glygen.org/publication/PubMed/9151714", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11828374", "url": "https://glygen.org/publication/PubMed/11828374", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "https://www.ebi.ac.uk/intact/interactors/id:P43403*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "16339550", "url": "https://glygen.org/publication/PubMed/16339550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P43403", "database": "PRO", "categories": [ "Other" ] }, { "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18779373", "url": "https://glygen.org/publication/PubMed/18779373", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30692994", "url": "https://glygen.org/publication/PubMed/30692994", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32974219", "url": "https://glygen.org/publication/PubMed/32974219", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EPARITSPDKPRPMPMDTSV", "down_seq": "ESPYSDPEELKDKKLFLKRD", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Increased constitutive kinase activity; when associated with F-319.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" }, { "database": "PubMed", "id": "9151714", "url": "https://glygen.org/publication/PubMed/9151714" }, { "database": "PubMed", "id": "11828374", "url": "https://glygen.org/publication/PubMed/11828374" } ] }, { "sequence_org": "Y", "sequence_mut": "F", "comment": "Increased constitutive kinase activity; when associated with F-319. About 75% loss of CD247/CD3Z-binding in stimulated TCR and complete loss of VAV1 interaction.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" }, { "database": "PubMed", "id": "9151714", "url": "https://glygen.org/publication/PubMed/9151714" }, { "database": "PubMed", "id": "11828374", "url": "https://glygen.org/publication/PubMed/11828374" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P43403-1", "kinase_gene_name": "ZAP70", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" }, { "database": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" }, { "database": "PubMed", "id": "11828374", "url": "https://glygen.org/publication/PubMed/11828374" } ], "site_lbl": "Tyr315" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by LCK", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "IntAct", "id": "P43403", "url": "https://www.ebi.ac.uk/intact/interactors/id:P43403*" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "16339550", "url": "https://glygen.org/publication/PubMed/16339550" }, { "database": "PubMed", "id": "9151714", "url": "https://glygen.org/publication/PubMed/9151714" }, { "database": "PRO", "id": "P43403", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P43403" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" }, { "database": "PubMed", "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606" }, { "database": "PubMed", "id": "18779373", "url": "https://glygen.org/publication/PubMed/18779373" }, { "database": "PubMed", "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055" }, { "database": "PubMed", "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330" }, { "database": "PubMed", "id": "30692994", "url": "https://glygen.org/publication/PubMed/30692994" }, { "database": "PubMed", "id": "32974219", "url": "https://glygen.org/publication/PubMed/32974219" } ], "site_lbl": "Tyr315" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P43403-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43403-1.304.304", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.314.314", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "P43403-1.315.319", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43403-1.319.319", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43403-1.327.327", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.315.319", "start_pos": 315, "end_pos": 319, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Chan AY, Punwani D, Kadlecek TA, Cowan MJ, Olson JL, Mathes EF, Sunderam U, Fu SM, Srinivasan R, Kuriyan J, Brenner SE, Weiss A, Puck JM", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "YESPY", "start_aa": "Y", "up_seq": "EPARITSPDKPRPMPMDTSV", "down_seq": "SDPEELKDKKLFLKRDNLLI", "mutagenesis": [ { "sequence_org": "YESPY", "sequence_mut": "AESPA", "comment": "Increases strongly constitutive kinase activity on LAT phosphorylation.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P43403-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43403-1.304.304", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.314.314", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "P43403-1.315.315", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 0, "direction": "upstream", "id": "P43403-1.319.319", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43403-1.327.327", "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": "P43403-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] }, { "title": "Tyrosine 319, a newly identified phosphorylation site of ZAP-70, plays a critical role in T cell antigen receptor signaling.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Di Bartolo V, Mege D, Germain V, Pelosi M, Dufour E, Michel F, Magistrelli G, Isacchi A, Acuto O", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" } ] }, { "title": "Requirement for Abl kinases in T cell receptor signaling.", "journal": "Current biology : CB", "date": "2004", "authors": "Zipfel PA, Zhang W, Quiroz M, Pendergast AM", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "15268851", "url": "https://glygen.org/publication/PubMed/15268851" } ] }, { "title": "Tyrosine 319 in the interdomain B of ZAP-70 is a binding site for the Src homology 2 domain of Lck.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Pelosi M, Di Bartolo V, Mounier V, Mege D, Pascussi JM, Dufour E, Blondel A, Acuto O", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "10318843", "url": "https://glygen.org/publication/PubMed/10318843" } ] }, { "title": "Phosphorylation of Tyr319 in ZAP-70 is required for T-cell antigen receptor-dependent phospholipase C-gamma1 and Ras activation.", "journal": "The EMBO journal", "date": "1999", "authors": "Williams BL, Irvin BJ, Sutor SL, Chini CC, Yacyshyn E, Bubeck Wardenburg J, Dalton M, Chan AC, Abraham RT", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "10202147", "url": "https://glygen.org/publication/PubMed/10202147" } ] }, { "title": "Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "Watts JD, Affolter M, Krebs DL, Wange RL, Samelson LE, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ] }, { "title": "Distinct tyrosine phosphorylation sites in ZAP-70 mediate activation and negative regulation of antigen receptor function.", "journal": "Molecular and cellular biology", "date": "1996", "authors": "Kong G, Dalton M, Bubeck Wardenburg J, Straus D, Kurosaki T, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ] }, { "title": "Insights into the suppressor of T-cell receptor (TCR) signaling-1 (Sts-1)-mediated regulation of TCR signaling through the use of novel substrate-trapping Sts-1 phosphatase variants.", "journal": "The FEBS journal", "date": "2014-02", "authors": "Luis Boris S, Carpino Nick", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "24256567", "url": "https://glygen.org/publication/PubMed/24256567" } ] }, { "title": "Requirement for tyrosine residues 315 and 319 within zeta chain-associated protein 70 for T cell development.", "journal": "The Journal of experimental medicine", "date": "2001", "authors": "Gong Q, Jin X, Akk AM, Foger N, White M, Gong G, Bubeck Wardenburg J, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606" } ] }, { "title": "CTLA-4 suppresses proximal TCR signaling in resting human CD4(+) T cells by inhibiting ZAP-70 Tyr(319) phosphorylation: a potential role for tyrosine phosphatases.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2002", "authors": "Guntermann C, Alexander DR", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "11970985", "url": "https://glygen.org/publication/PubMed/11970985" } ] }, { "title": "Inhibition of T cell receptor signal transduction by tyrosine kinase-interacting protein of Herpesvirus saimiri.", "journal": "The Journal of experimental medicine", "date": "2004", "authors": "Cho NH, Feng P, Lee SH, Lee BS, Liang X, Chang H, Jung JU", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "15337788", "url": "https://glygen.org/publication/PubMed/15337788" } ] }, { "title": "ZAP-70 tyrosine kinase is constitutively expressed and phosphorylated in B-lineage acute lymphoblastic leukemia cells.", "journal": "Haematologica", "date": "2005", "authors": "Guillaume N, Alleaume C, Munfus D, Capiod JC, Touati G, Pautard B, Desablens B, Lefrere JJ, Gouilleux F, Lassoued K, Gouilleux-Gruart V", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "15996927", "url": "https://glygen.org/publication/PubMed/15996927" } ] }, { "title": "CXCR3-mediated T-cell chemotaxis involves ZAP-70 and is regulated by signalling through the T-cell receptor.", "journal": "Immunology", "date": "2007", "authors": "Dar WA, Knechtle SJ", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "17250586", "url": "https://glygen.org/publication/PubMed/17250586" } ] }, { "title": "A novel small molecule inhibitor of signal transducers and activators of transcription 3 reverses immune tolerance in malignant glioma patients.", "journal": "Cancer research", "date": "2007", "authors": "Hussain SF, Kong LY, Jordan J, Conrad C, Madden T, Fokt I, Priebe W, Heimberger AB", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "17942891", "url": "https://glygen.org/publication/PubMed/17942891" } ] }, { "title": "c-Abl is required for the signaling transduction induced by L-selectin ligation.", "journal": "European journal of immunology", "date": "2007", "authors": "Chen C, Shang X, Xu T, Cui L, Luo J, Ba X, Hao S, Zeng X", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "17960665", "url": "https://glygen.org/publication/PubMed/17960665" } ] }, { "title": "Inhibition of ZAP-70 kinase activity via an analog-sensitive allele blocks T cell receptor and CD28 superagonist signaling.", "journal": "The Journal of biological chemistry", "date": "2008", "authors": "Levin SE, Zhang C, Kadlecek TA, Shokat KM, Weiss A", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "18378687", "url": "https://glygen.org/publication/PubMed/18378687" } ] }, { "title": "The nonphagocytic NADPH oxidase Duox1 mediates a positive feedback loop during T cell receptor signaling.", "journal": "Science signaling", "date": "2010", "authors": "Kwon J, Shatynski KE, Chen H, Morand S, de Deken X, Miot F, Leto TL, Williams MS", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "20682913", "url": "https://glygen.org/publication/PubMed/20682913" } ] }, { "title": "RhoH regulates subcellular localization of ZAP-70 and Lck in T cell receptor signaling.", "journal": "PloS one", "date": "2010", "authors": "Chae HD, Siefring JE, Hildeman DA, Gu Y, Williams DA", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055" } ] }, { "title": "F-actin polymerization and retrograde flow drive sustained PLCgamma1 signaling during T cell activation.", "journal": "The Journal of cell biology", "date": "2012", "authors": "Babich A, Li S, O'Connor RS, Milone MC, Freedman BD, Burkhardt JK", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "22665519", "url": "https://glygen.org/publication/PubMed/22665519" } ] }, { "title": "CD25 and CD69 induction by alpha4beta1 outside-in signalling requires TCR early signalling complex proteins.", "journal": "The Biochemical journal", "date": "2013", "authors": "Cimo AM, Ahmed Z, McIntyre BW, Lewis DE, Ladbury JE", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23758320", "url": "https://glygen.org/publication/PubMed/23758320" } ] }, { "title": "A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Chan AY, Punwani D, Kadlecek TA, Cowan MJ, Olson JL, Mathes EF, Sunderam U, Fu SM, Srinivasan R, Kuriyan J, Brenner SE, Weiss A, Puck JM", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] }, { "title": "The Size of Activating and Inhibitory Killer Ig-like Receptor Nanoclusters Is Controlled by the Transmembrane Sequence and Affects Signaling.", "journal": "Cell reports", "date": "2016", "authors": "Oszmiana A, Williamson DJ, Cordoba SP, Morgan DJ, Kennedy PR, Stacey K, Davis DM", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "27210755", "url": "https://glygen.org/publication/PubMed/27210755" } ] }, { "title": "A Stretch of Negatively Charged Amino Acids of Linker for Activation of T-Cell Adaptor Has a Dual Role in T-Cell Antigen Receptor Intracellular Signaling.", "journal": "Frontiers in immunology", "date": "2018", "authors": "Arbulo-Echevarria MM, Narbona-Sanchez I, Fernandez-Ponce CM, Vico-Barranco I, Rueda-Ygueravide MD, Dustin ML, Miazek A, Duran-Ruiz MC, Garcia-Cozar F, Aguado E", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "29456532", "url": "https://glygen.org/publication/PubMed/29456532" } ] }, { "title": "Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70 to LAT.", "journal": "Nature immunology", "date": "2018", "authors": "Lo WL, Shah NH, Ahsan N, Horkova V, Stepanek O, Salomon AR, Kuriyan J, Weiss A", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "29915297", "url": "https://glygen.org/publication/PubMed/29915297" } ] }, { "title": "Mathematical modeling identifies Lck as a potential mediator for PD-1 induced inhibition of early TCR signaling.", "journal": "PloS one", "date": "2018", "authors": "Arulraj T, Barik D", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330" } ] }, { "title": "CD103 Promotes the Pro-inflammatory Response of Gastric Resident CD4+ T Cell in Helicobacter pylori-Positive Gastritis.", "journal": "Frontiers in cellular and infection microbiology", "date": "2020", "authors": "Chen Peiyu, Ming Siqi, Lao Juanfeng, Li Chunna, Wang Hongli, Xiong Liya, Zhang Shunxian, Liang Zibin, Niu Xiaoli, Deng Simei, Geng Lanlan, Wu Minhao, Wu Yongjian, Gong Sitang", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "32974219", "url": "https://glygen.org/publication/PubMed/32974219" } ] }, { "title": "Tyrosine 192 within the SH2 domain of the Src-protein tyrosine kinase p56Lck regulates T-cell activation independently of Lck/CD45 interactions.", "journal": "Cell communication and signaling : CCS", "date": "2020-11-23", "authors": "K\u00e4stle Matthias, Merten Camilla, Hartig Roland, Kaehne Thilo, Liaunardy-Jopeace Ardiyanto, Woessner Nadine M, Schamel Wolfgang W, James John, Minguet Susana, Simeoni Luca, Schraven Burkhart", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "33225946", "url": "https://glygen.org/publication/PubMed/33225946" } ] }, { "title": "T cell receptor-dependent S-acylation of ZAP-70 controls activation of T cells.", "journal": "The Journal of biological chemistry", "date": "2021", "authors": "Tewari Ritika, Shayahati Bieerkehazhi, Fan Ying, Akimzhanov Askar M", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "33482200", "url": "https://glygen.org/publication/PubMed/33482200" } ] }, { "title": "Cooperative Interaction of Nck and Lck Orchestrates Optimal TCR Signaling.", "journal": "Cells", "date": "2021", "authors": "Hartl FA, Ngoenkam J, Beck-Garcia E, Cerqueira L, Wipa P, Paensuwan P, Suriyaphol P, Mishra P, Schraven B, Gunther S, Pongcharoen S, Schamel WWA, Minguet S", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "33917227", "url": "https://glygen.org/publication/PubMed/33917227" } ] }, { "title": "A Cysteine Residue within the Kinase Domain of Zap70 Regulates Lck Activity and Proximal TCR Signaling.", "journal": "Cells", "date": "2022", "authors": "Schultz A, Schnurra M, El-Bizri A, Woessner NM, Hartmann S, Hartig R, Minguet S, Schraven B, Simeoni L", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "36078131", "url": "https://glygen.org/publication/PubMed/36078131" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15268851", "url": "https://glygen.org/publication/PubMed/15268851", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10318843", "url": "https://glygen.org/publication/PubMed/10318843", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10202147", "url": "https://glygen.org/publication/PubMed/10202147", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "https://www.ebi.ac.uk/intact/interactors/id:P43403*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "24256567", "url": "https://glygen.org/publication/PubMed/24256567", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11970985", "url": "https://glygen.org/publication/PubMed/11970985", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15337788", "url": "https://glygen.org/publication/PubMed/15337788", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15996927", "url": "https://glygen.org/publication/PubMed/15996927", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17250586", "url": "https://glygen.org/publication/PubMed/17250586", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17942891", "url": "https://glygen.org/publication/PubMed/17942891", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17960665", "url": "https://glygen.org/publication/PubMed/17960665", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18378687", "url": "https://glygen.org/publication/PubMed/18378687", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20682913", "url": "https://glygen.org/publication/PubMed/20682913", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22665519", "url": "https://glygen.org/publication/PubMed/22665519", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23758320", "url": "https://glygen.org/publication/PubMed/23758320", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27210755", "url": "https://glygen.org/publication/PubMed/27210755", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29456532", "url": "https://glygen.org/publication/PubMed/29456532", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29915297", "url": "https://glygen.org/publication/PubMed/29915297", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32974219", "url": "https://glygen.org/publication/PubMed/32974219", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33225946", "url": "https://glygen.org/publication/PubMed/33225946", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33482200", "url": "https://glygen.org/publication/PubMed/33482200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33917227", "url": "https://glygen.org/publication/PubMed/33917227", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36078131", "url": "https://glygen.org/publication/PubMed/36078131", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ITSPDKPRPMPMDTSVYESP", "down_seq": "SDPEELKDKKLFLKRDNLLI", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Increased constitutive kinase activity; when associated with F-315.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" } ] }, { "sequence_org": "Y", "sequence_mut": "F", "comment": "Increased constitutive kinase activity; when associated with F-315. About 80% loss of TCR-induced NFAT activation.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00519-1", "kinase_gene_name": "ABL1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "15268851", "url": "https://glygen.org/publication/PubMed/15268851" } ], "site_lbl": "Tyr319" }, { "kinase_uniprot_canonical_ac": "P06239-1", "kinase_gene_name": "LCK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "10318843", "url": "https://glygen.org/publication/PubMed/10318843" }, { "database": "PubMed", "id": "10202147", "url": "https://glygen.org/publication/PubMed/10202147" } ], "site_lbl": "Tyr319" }, { "kinase_uniprot_canonical_ac": "P43403-1", "kinase_gene_name": "ZAP70", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" }, { "database": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ], "site_lbl": "Tyr319" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" }, { "database": "IntAct", "id": "P43403", "url": "https://www.ebi.ac.uk/intact/interactors/id:P43403*" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "10318843", "url": "https://glygen.org/publication/PubMed/10318843" }, { "database": "PubMed", "id": "24256567", "url": "https://glygen.org/publication/PubMed/24256567" }, { "database": "PubMed", "id": "10202147", "url": "https://glygen.org/publication/PubMed/10202147" }, { "database": "PubMed", "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606" }, { "database": "PubMed", "id": "11970985", "url": "https://glygen.org/publication/PubMed/11970985" }, { "database": "PubMed", "id": "15337788", "url": "https://glygen.org/publication/PubMed/15337788" }, { "database": "PubMed", "id": "15996927", "url": "https://glygen.org/publication/PubMed/15996927" }, { "database": "PubMed", "id": "17250586", "url": "https://glygen.org/publication/PubMed/17250586" }, { "database": "PubMed", "id": "17942891", "url": "https://glygen.org/publication/PubMed/17942891" }, { "database": "PubMed", "id": "17960665", "url": "https://glygen.org/publication/PubMed/17960665" }, { "database": "PubMed", "id": "18378687", "url": "https://glygen.org/publication/PubMed/18378687" }, { "database": "PubMed", "id": "20682913", "url": "https://glygen.org/publication/PubMed/20682913" }, { "database": "PubMed", "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055" }, { "database": "PubMed", "id": "22665519", "url": "https://glygen.org/publication/PubMed/22665519" }, { "database": "PubMed", "id": "23758320", "url": "https://glygen.org/publication/PubMed/23758320" }, { "database": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" }, { "database": "PubMed", "id": "27210755", "url": "https://glygen.org/publication/PubMed/27210755" }, { "database": "PubMed", "id": "29456532", "url": "https://glygen.org/publication/PubMed/29456532" }, { "database": "PubMed", "id": "29915297", "url": "https://glygen.org/publication/PubMed/29915297" }, { "database": "PubMed", "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330" }, { "database": "PubMed", "id": "32974219", "url": "https://glygen.org/publication/PubMed/32974219" }, { "database": "PubMed", "id": "33225946", "url": "https://glygen.org/publication/PubMed/33225946" }, { "database": "PubMed", "id": "33482200", "url": "https://glygen.org/publication/PubMed/33482200" }, { "database": "PubMed", "id": "33917227", "url": "https://glygen.org/publication/PubMed/33917227" }, { "database": "PubMed", "id": "36078131", "url": "https://glygen.org/publication/PubMed/36078131" } ], "site_lbl": "Tyr319" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P43403-1.304.304", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43403-1.314.314", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43403-1.315.315", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 0, "direction": "downstream", "id": "P43403-1.315.319", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43403-1.327.327", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": 4 } ], "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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.327.327", "start_pos": 327, "end_pos": 327, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Chan AY, Punwani D, Kadlecek TA, Cowan MJ, Olson JL, Mathes EF, Sunderam U, Fu SM, Srinivasan R, Kuriyan J, Brenner SE, Weiss A, Puck JM", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PMPMDTSVYESPYSDPEELK", "down_seq": "KKLFLKRDNLLIADIELGCG", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "P", "comment": "Increases constitutive kinase activity on LAT phosphorylation, strongly increases subcellular localization of CD69 at the cell surface and decreases autoinhibition conformation.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P43403-1.314.314", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43403-1.315.315", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43403-1.315.319", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43403-1.319.319", "categories": [ "mutagenesis_flag", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.362.362", "start_pos": 362, "end_pos": 362, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Chan AY, Punwani D, Kadlecek TA, Cowan MJ, Olson JL, Mathes EF, Sunderam U, Fu SM, Srinivasan R, Kuriyan J, Brenner SE, Weiss A, Puck JM", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IELGCGNFGSVRQGVYRMRK", "down_seq": "QIDVAIKVLKQGTEKADTEE", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "E", "comment": "Increases constitutive kinase activity on LAT phosphorylation, strongly increases subcellular localization of CD69 at the cell surface and decreases autoinhibition conformation.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P43403-1.358.358", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43403-1.360.360", "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": "P43403-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Chan AY, Punwani D, Kadlecek TA, Cowan MJ, Olson JL, Mathes EF, Sunderam U, Fu SM, Srinivasan R, Kuriyan J, Brenner SE, Weiss A, Puck JM", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RAEAEEHLKLAGMADGLFLL", "down_seq": "QCLRSLGGYVLSLVHDVRFH", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "K", "comment": "Decreases interaction with phosphorylated CD247; when associated with K-190.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] } ], "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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": "2", "chr_pos": "97724146", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R37", "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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P43403-1.27.27", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "P43403-1.461.461", "start_pos": 461, "end_pos": 461, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLHQVSMGMKYLEEKNFVHR", "down_seq": "LAARNVLLVNRHYAKISDFG", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "N", "comment": "Abolishes kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P43403-1.465.465", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43403-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43403-1.479.479", "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": "P43403-1.479.479", "start_pos": 479, "end_pos": 479, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The three-dimensional structure of the ZAP-70 kinase domain in complex with staurosporine: implications for the design of selective inhibitors.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Jin L, Pluskey S, Petrella EC, Cantin SM, Gorga JC, Rynkiewicz MJ, Pandey P, Strickler JE, Babine RE, Weaver DT, Seidl KJ", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "15292186", "url": "https://glygen.org/publication/PubMed/15292186" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15292186", "url": "https://glygen.org/publication/PubMed/15292186", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HRDLAARNVLLVNRHYAKIS", "down_seq": "FGLSKALGADDSYYTARSAG", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "N", "comment": "Abolishes kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "15292186", "url": "https://glygen.org/publication/PubMed/15292186" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43403-1.461.461", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43403-1.465.465", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43403-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43403-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43403-1.492.492", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43403-1.493.493", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43403-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43403-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43403-1.497.497", "categories": [ "glycosylation_flag", "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": "P43403-1.492.492", "start_pos": 492, "end_pos": 492, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Activation of ZAP-70 kinase activity by phosphorylation of tyrosine 493 is required for lymphocyte antigen receptor function.", "journal": "The EMBO journal", "date": "1995", "authors": "Chan AC, Dalton M, Johnson R, Kong GH, Wang T, Thoma R, Kurosaki T", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "7781602", "url": "https://glygen.org/publication/PubMed/7781602" } ] }, { "title": "Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "Watts JD, Affolter M, Krebs DL, Wange RL, Samelson LE, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ] }, { "title": "Distinct tyrosine phosphorylation sites in ZAP-70 mediate activation and negative regulation of antigen receptor function.", "journal": "Molecular and cellular biology", "date": "1996", "authors": "Kong G, Dalton M, Bubeck Wardenburg J, Straus D, Kurosaki T, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ] }, { "title": "Activating and inhibitory mutations in adjacent tyrosines in the kinase domain of ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Wange RL, Guitian R, Isakov N, Watts JD, Aebersold R, Samelson LE", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "7642520", "url": "https://glygen.org/publication/PubMed/7642520" } ] }, { "title": "Analysis of regulatory phosphorylation sites in ZAP-70 by capillary high-performance liquid chromatography coupled to electrospray ionization or matrix-assisted laser desorption ionization time-of-flight mass spectrometry.", "journal": "Journal of chromatography. B, Biomedical sciences and applications", "date": "2001", "authors": "Miliotis T, Ericsson PO, Marko-Varga G, Svensson R, Nilsson J, Laurell T, Bischoff R", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "11270871", "url": "https://glygen.org/publication/PubMed/11270871" } ] }, { "title": "CBAP functions as a novel component in chemokine-induced ZAP70-mediated T-cell adhesion and migration.", "journal": "PloS one", "date": "2013", "authors": "Chiang YJ, Ho KC, Sun CT, Chiu JJ, Lee FJ, Liao F, Yang-Yen HF, Yen JJ", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23620790", "url": "https://glygen.org/publication/PubMed/23620790" } ] }, { "title": "ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells.", "journal": "PloS one", "date": "2013", "authors": "Helou YA, Nguyen V, Beik SP, Salomon AR", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" } ] }, { "title": "ZAP-70 protein tyrosine kinase is constitutively targeted to the T cell cortex independently of its SH2 domains.", "journal": "The Journal of cell biology", "date": "1997", "authors": "Huby RD, Iwashima M, Weiss A, Ley SC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7781602", "url": "https://glygen.org/publication/PubMed/7781602", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7642520", "url": "https://glygen.org/publication/PubMed/7642520", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11270871", "url": "https://glygen.org/publication/PubMed/11270871", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23620790", "url": "https://glygen.org/publication/PubMed/23620790", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RHYAKISDFGLSKALGADDS", "down_seq": "YTARSAGKWPLKWYAPECIN", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Increases kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "7781602", "url": "https://glygen.org/publication/PubMed/7781602" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06239-1", "kinase_gene_name": "LCK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" }, { "database": "PubMed", "id": "7642520", "url": "https://glygen.org/publication/PubMed/7642520" } ], "site_lbl": "Tyr492" }, { "kinase_uniprot_canonical_ac": "P43403-1", "kinase_gene_name": "ZAP70", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ], "site_lbl": "Tyr492" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "7781602", "url": "https://glygen.org/publication/PubMed/7781602" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "11270871", "url": "https://glygen.org/publication/PubMed/11270871" }, { "database": "PubMed", "id": "23620790", "url": "https://glygen.org/publication/PubMed/23620790" }, { "database": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177" } ], "site_lbl": "Tyr492" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43403-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43403-1.479.479", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43403-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.493.493", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43403-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43403-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43403-1.497.497", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": 3 } ], "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": "P43403-1.493.493", "start_pos": 493, "end_pos": 493, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Activation of ZAP-70 kinase activity by phosphorylation of tyrosine 493 is required for lymphocyte antigen receptor function.", "journal": "The EMBO journal", "date": "1995", "authors": "Chan AC, Dalton M, Johnson R, Kong GH, Wang T, Thoma R, Kurosaki T", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "7781602", "url": "https://glygen.org/publication/PubMed/7781602" } ] }, { "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": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] }, { "title": "Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "Watts JD, Affolter M, Krebs DL, Wange RL, Samelson LE, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ] }, { "title": "Distinct tyrosine phosphorylation sites in ZAP-70 mediate activation and negative regulation of antigen receptor function.", "journal": "Molecular and cellular biology", "date": "1996", "authors": "Kong G, Dalton M, Bubeck Wardenburg J, Straus D, Kurosaki T, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ] }, { "title": "Determination of regulatory phosphorylation sites in nanogram amounts of a synthetic fragment of ZAP-70 using microprobe NMR and on-line coupled capillary HPLC-NMR.", "journal": "Magnetic resonance in chemistry : MRC", "date": "2005", "authors": "Hentschel P, Krucker M, Grynbaum MD, Putzbach K, Bischoff R, Albert K", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "16049944", "url": "https://glygen.org/publication/PubMed/16049944" } ] }, { "title": "Analysis of regulatory phosphorylation sites in ZAP-70 by capillary high-performance liquid chromatography coupled to electrospray ionization or matrix-assisted laser desorption ionization time-of-flight mass spectrometry.", "journal": "Journal of chromatography. B, Biomedical sciences and applications", "date": "2001", "authors": "Miliotis T, Ericsson PO, Marko-Varga G, Svensson R, Nilsson J, Laurell T, Bischoff R", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "11270871", "url": "https://glygen.org/publication/PubMed/11270871" } ] }, { "title": "Requirement for tyrosine residues 315 and 319 within zeta chain-associated protein 70 for T cell development.", "journal": "The Journal of experimental medicine", "date": "2001", "authors": "Gong Q, Jin X, Akk AM, Foger N, White M, Gong G, Bubeck Wardenburg J, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606" } ] }, { "title": "Activation of ZAP-70 through specific dephosphorylation at the inhibitory Tyr-292 by the low molecular weight phosphotyrosine phosphatase (LMPTP).", "journal": "The Journal of biological chemistry", "date": "2002", "authors": "Bottini N, Stefanini L, Williams S, Alonso A, Jascur T, Abraham RT, Couture C, Mustelin T", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "11976341", "url": "https://glygen.org/publication/PubMed/11976341" } ] }, { "title": "Intracellular Phospho-Flow cytometry reveals novel insights into TCR proximal signaling events. A comparison with Western blot.", "journal": "Cytometry. Part A : the journal of the International Society for Analytical Cytology", "date": "2008", "authors": "Haas A, Weckbecker G, Welzenbach K", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "18548611", "url": "https://glygen.org/publication/PubMed/18548611" } ] }, { "title": "RhoH regulates subcellular localization of ZAP-70 and Lck in T cell receptor signaling.", "journal": "PloS one", "date": "2010", "authors": "Chae HD, Siefring JE, Hildeman DA, Gu Y, Williams DA", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055" } ] }, { "title": "A new pathway of CD5 glycoprotein-mediated T cell inhibition dependent on inhibitory phosphorylation of Fyn kinase.", "journal": "The Journal of biological chemistry", "date": "2011", "authors": "Bamberger M, Santos AM, Goncalves CM, Oliveira MI, James JR, Moreira A, Lozano F, Davis SJ, Carmo AM", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "21757751", "url": "https://glygen.org/publication/PubMed/21757751" } ] }, { "title": "CD25 and CD69 induction by alpha4beta1 outside-in signalling requires TCR early signalling complex proteins.", "journal": "The Biochemical journal", "date": "2013", "authors": "Cimo AM, Ahmed Z, McIntyre BW, Lewis DE, Ladbury JE", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23758320", "url": "https://glygen.org/publication/PubMed/23758320" } ] }, { "title": "ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells.", "journal": "PloS one", "date": "2013", "authors": "Helou YA, Nguyen V, Beik SP, Salomon AR", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" } ] }, { "title": "Memory CD8+ T cells exhibit increased antigen threshold requirements for recall proliferation.", "journal": "The Journal of experimental medicine", "date": "2014", "authors": "Mehlhop-Williams ER, Bevan MJ", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "24493801", "url": "https://glygen.org/publication/PubMed/24493801" } ] }, { "title": "A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Chan AY, Punwani D, Kadlecek TA, Cowan MJ, Olson JL, Mathes EF, Sunderam U, Fu SM, Srinivasan R, Kuriyan J, Brenner SE, Weiss A, Puck JM", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" } ] }, { "title": "Non-degradative Ubiquitination of Protein Kinases.", "journal": "PLoS computational biology", "date": "2016", "authors": "Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "27253329", "url": "https://glygen.org/publication/PubMed/27253329" } ] }, { "title": "Mathematical modeling identifies Lck as a potential mediator for PD-1 induced inhibition of early TCR signaling.", "journal": "PloS one", "date": "2018", "authors": "Arulraj T, Barik D", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330" } ] }, { "title": "T cell receptor-dependent S-acylation of ZAP-70 controls activation of T cells.", "journal": "The Journal of biological chemistry", "date": "2021", "authors": "Tewari Ritika, Shayahati Bieerkehazhi, Fan Ying, Akimzhanov Askar M", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "33482200", "url": "https://glygen.org/publication/PubMed/33482200" } ] }, { "title": "ZAP-70 protein tyrosine kinase is constitutively targeted to the T cell cortex independently of its SH2 domains.", "journal": "The Journal of cell biology", "date": "1997", "authors": "Huby RD, Iwashima M, Weiss A, Ley SC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7781602", "url": "https://glygen.org/publication/PubMed/7781602", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16049944", "url": "https://glygen.org/publication/PubMed/16049944", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P43403", "database": "PRO", "categories": [ "Other" ] }, { "id": "11270871", "url": "https://glygen.org/publication/PubMed/11270871", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11976341", "url": "https://glygen.org/publication/PubMed/11976341", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18548611", "url": "https://glygen.org/publication/PubMed/18548611", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21757751", "url": "https://glygen.org/publication/PubMed/21757751", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23758320", "url": "https://glygen.org/publication/PubMed/23758320", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24493801", "url": "https://glygen.org/publication/PubMed/24493801", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27253329", "url": "https://glygen.org/publication/PubMed/27253329", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33482200", "url": "https://glygen.org/publication/PubMed/33482200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "HYAKISDFGLSKALGADDSY", "down_seq": "TARSAGKWPLKWYAPECINF", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Impairs kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "7781602", "url": "https://glygen.org/publication/PubMed/7781602" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06239-1", "kinase_gene_name": "LCK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ], "site_lbl": "Tyr493" }, { "kinase_uniprot_canonical_ac": "P43403-1", "kinase_gene_name": "ZAP70", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "16049944", "url": "https://glygen.org/publication/PubMed/16049944" } ], "site_lbl": "Tyr493" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "7781602", "url": "https://glygen.org/publication/PubMed/7781602" }, { "database": "PRO", "id": "P43403", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P43403" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "11270871", "url": "https://glygen.org/publication/PubMed/11270871" }, { "database": "PubMed", "id": "11514606", "url": "https://glygen.org/publication/PubMed/11514606" }, { "database": "PubMed", "id": "11976341", "url": "https://glygen.org/publication/PubMed/11976341" }, { "database": "PubMed", "id": "18548611", "url": "https://glygen.org/publication/PubMed/18548611" }, { "database": "PubMed", "id": "21103055", "url": "https://glygen.org/publication/PubMed/21103055" }, { "database": "PubMed", "id": "21757751", "url": "https://glygen.org/publication/PubMed/21757751" }, { "database": "PubMed", "id": "23758320", "url": "https://glygen.org/publication/PubMed/23758320" }, { "database": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" }, { "database": "PubMed", "id": "24493801", "url": "https://glygen.org/publication/PubMed/24493801" }, { "database": "PubMed", "id": "26783323", "url": "https://glygen.org/publication/PubMed/26783323" }, { "database": "PubMed", "id": "27253329", "url": "https://glygen.org/publication/PubMed/27253329" }, { "database": "PubMed", "id": "30356330", "url": "https://glygen.org/publication/PubMed/30356330" }, { "database": "PubMed", "id": "33482200", "url": "https://glygen.org/publication/PubMed/33482200" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "9199177", "url": "https://glygen.org/publication/PubMed/9199177" } ], "site_lbl": "Tyr493" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43403-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43403-1.479.479", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43403-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.492.492", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43403-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43403-1.497.497", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": 3 } ], "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": 19 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.538.538", "start_pos": 538, "end_pos": 538, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Otud7b facilitates T cell activation and inflammatory responses by regulating Zap70 ubiquitination.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Hu H, Wang H, Xiao Y, Jin J, Chang JH, Zou Q, Xie X, Cheng X, Sun SC", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SRSDVWSYGVTMWEALSYGQ", "down_seq": "PYKKMKGPEVMAFIEQGKRM", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "No effect on ubiquitination.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43403-1.520.520", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43403-1.521.521", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43403-1.544.544", "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": "P43403-1.544.544", "start_pos": 544, "end_pos": 544, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Otud7b facilitates T cell activation and inflammatory responses by regulating Zap70 ubiquitination.", "journal": "The Journal of experimental medicine", "date": "2016", "authors": "Hu H, Wang H, Xiao Y, Jin J, Chang JH, Zou Q, Xie X, Cheng X, Sun SC", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SYGVTMWEALSYGQKPYKKM", "down_seq": "GPEVMAFIEQGKRMECPPEC", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Strongly decreased ubiquitination.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "26903241", "url": "https://glygen.org/publication/PubMed/26903241" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P43403-1.538.538", "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": "P43403-1.597.597", "start_pos": 597, "end_pos": 597, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IYKWEDRPDFLTVEQRMRAC", "down_seq": "YSLASKVEGPPGSTQKAEAA", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Increased kinase activity after activation by LCK.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P43403-1.598.598", "categories": [ "mutagenesis_flag", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.598.598", "start_pos": 598, "end_pos": 598, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "journal": "Cell", "date": "2007", "authors": "Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, Kuriyan J", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "reference": [ { "type": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] }, { "title": "ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells.", "journal": "PloS one", "date": "2013", "authors": "Helou YA, Nguyen V, Beik SP, Salomon AR", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YKWEDRPDFLTVEQRMRACY", "down_seq": "SLASKVEGPPGSTQKAEAAC", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Increased kinase activity after activation by LCK.", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "17512407", "url": "https://glygen.org/publication/PubMed/17512407" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" } ], "site_lbl": "Tyr598" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P43403-1.597.597", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": "P43403-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RKPCNRPSGLEPQPGVFDCL", "down_seq": "DAMVRDYVRQTWKLEGEALE", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "97724391", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R119", "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": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43403-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43403-1.126.126", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43403-1.131.131", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43403-1.133.133", "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": "P43403-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1559319806", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1559319806", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1559319806", "url": "https://www.ensembl.org/id/rs1559319806", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MPDPAAHLPFFYG", "down_seq": "ISRAEAEEHLKLAGMADGLF", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" }, { "id": "rs1559319806", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1559319806" }, { "id": "rs1559319806", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1559319806" } ], "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 (SIS->NIS).", "chr_id": "2", "chr_pos": "97724077", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S14", "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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P43403-1.27.27", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43403-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "EQAIISQAPQVEKLIATTAH", "down_seq": "RMPWYHSSLTREEAERKLYS", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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 (3).", "chr_id": "2", "chr_pos": "97725164", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E159", "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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43403-1.141.141", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43403-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43403-1.145.145", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43403-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43403-1.178.178", "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": "P43403-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EEAERKLYSGAQTDGKFLLR", "down_seq": "RKEQGTYALSLIYGKTVYHY", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "97732891", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P191", "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: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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P43403-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.190.190", "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": "P43403-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HLPFFYGSISRAEAEEHLKL", "down_seq": "GMADGLFLLRQCLRSLGGYV", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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": "2", "chr_pos": "97724116", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A27", "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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P43403-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43403-1.37.37", "categories": [ "mutagenesis_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": "P43403-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "THPQRRIDTLNSDGYTPEPA", "down_seq": "ITSPDKPRPMPMDTSVYESP", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "97734522", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R298", "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: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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P43403-1.289.289", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43403-1.292.292", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43403-1.293.293", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43403-1.304.304", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43403-1.314.314", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43403-1.315.315", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43403-1.315.319", "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": "P43403-1.358.358", "start_pos": 358, "end_pos": 358, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LIADIELGCGNFGSVRQGVY", "down_seq": "MRKKQIDVAIKVLKQGTEKA", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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": "2", "chr_pos": "97734703", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R358", "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: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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P43403-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43403-1.362.362", "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": "P43403-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ADIELGCGNFGSVRQGVYRM", "down_seq": "KKQIDVAIKVLKQGTEKADT", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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 (3).", "chr_id": "2", "chr_pos": "97734708", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R360", "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" } ] }, { "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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P43403-1.358.358", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43403-1.362.362", "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": "P43403-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VAIKVLKQGTEKADTEEMMR", "down_seq": "AQIMHQLDNPYIVRLIGVCQ", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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 (3).", "chr_id": "2", "chr_pos": "97735323", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E386", "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: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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P43403-1.397.397", "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": "P43403-1.465.465", "start_pos": 465, "end_pos": 465, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VSMGMKYLEEKNFVHRDLAA", "down_seq": "NVLLVNRHYAKISDFGLSKA", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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": "2", "chr_pos": "97737577", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R465", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P43403-1.461.461", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43403-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43403-1.479.479", "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": "P43403-1.489.489", "start_pos": 489, "end_pos": 489, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1238614221", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1238614221", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1238614221", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1238614221#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1238614221", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1238614221", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LVNRHYAKISDFGLSKALGA", "down_seq": "DSYYTARSAGKWPLKWYAPE", "snv": [ { "evidence": [ { "id": "rs1238614221", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1238614221" }, { "id": "rs1238614221", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1238614221#frequency_tab" }, { "id": "rs1238614221", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1238614221" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "2", "chr_pos": "97737648", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D489", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P43403-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43403-1.479.479", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43403-1.492.492", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43403-1.493.493", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43403-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43403-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43403-1.497.497", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43403-1.496.496", "start_pos": 496, "end_pos": 496, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KISDFGLSKALGADDSYYTA", "down_seq": "SAGKWPLKWYAPECINFRKF", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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 (3).", "chr_id": "2", "chr_pos": "97737761", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R496", "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: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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P43403-1.479.479", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43403-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43403-1.492.492", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43403-1.493.493", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43403-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.497.497", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43403-1.514.514", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43403-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DDSYYTARSAGKWPLKWYAP", "down_seq": "CINFRKFSSRSDVWSYGVTM", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "2", "chr_pos": "97737799", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E509", "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: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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43403-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43403-1.492.492", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43403-1.493.493", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43403-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43403-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43403-1.497.497", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43403-1.514.514", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43403-1.520.520", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43403-1.521.521", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43403-1.514.514", "start_pos": 514, "end_pos": 514, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1264564157", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1264564157", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1264564157", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1264564157", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TARSAGKWPLKWYAPECINF", "down_seq": "KFSSRSDVWSYGVTMWEALS", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" }, { "id": "rs1264564157", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1264564157" }, { "id": "rs1264564157", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1264564157" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NFR->NFC).", "chr_id": "2", "chr_pos": "97737814", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R514", "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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43403-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43403-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43403-1.497.497", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43403-1.520.520", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43403-1.521.521", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43403-1.521.521", "start_pos": 521, "end_pos": 521, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "WPLKWYAPECINFRKFSSRS", "down_seq": "VWSYGVTMWEALSYGQKPYK", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "97737835", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D521", "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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43403-1.514.514", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.520.520", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43403-1.538.538", "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": "P43403-1.567.567", "start_pos": 567, "end_pos": 567, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "EVMAFIEQGKRMECPPECPP", "down_seq": "LYALMSDCWIYKWEDRPDFL", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "97738070", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E567", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P43403-1.573.573", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43403-1.573.573", "start_pos": 573, "end_pos": 573, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1357191899", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357191899", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1357191899", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1357191899#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1357191899", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357191899", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EQGKRMECPPECPPELYALM", "down_seq": "DCWIYKWEDRPDFLTVEQRM", "snv": [ { "evidence": [ { "id": "rs1357191899", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357191899" }, { "id": "rs1357191899", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1357191899#frequency_tab" }, { "id": "rs1357191899", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357191899" } ], "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": "2", "chr_pos": "97738089", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S573", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P43403-1.567.567", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43403-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LVHDVRFHHFPIERQLNGTY", "down_seq": "IAGGKAHCGPAELCEFYSRD", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "97724244", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A70", "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: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": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P43403-1.69.69", "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": "P43403-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GGKAHCGPAELCEFYSRDPD", "down_seq": "LPCNLRKPCNRPSGLEPQPG", "snv": [ { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "2", "chr_pos": "97724314", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G93", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P43403-1.99.99", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "P43403-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758557607", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758557607", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758557607", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758557607", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758557607", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758557607", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43403", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GPAELCEFYSRDPDGLPCNL", "down_seq": "KPCNRPSGLEPQPGVFDCLR", "snv": [ { "evidence": [ { "id": "rs758557607", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758557607" }, { "id": "rs758557607", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758557607" }, { "id": "rs758557607", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758557607" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLR->NLC).", "chr_id": "2", "chr_pos": "97724331", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R99", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43403", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43403" } ], "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": "2", "chr_pos": "97724332", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R99", "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" ] }, { "evidence": [ { "id": "rs758557607", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758557607" }, { "id": "rs758557607", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758557607" }, { "id": "rs758557607", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758557607" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLR->NLS).", "chr_id": "2", "chr_pos": "97724331", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R99", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P43403-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43403-1.119.119", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43403-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "Watts JD, Affolter M, Krebs DL, Wange RL, Samelson LE, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ] }, { "title": "Tyrosine 319, a newly identified phosphorylation site of ZAP-70, plays a critical role in T cell antigen receptor signaling.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Di Bartolo V, Mege D, Germain V, Pelosi M, Dufour E, Michel F, Magistrelli G, Isacchi A, Acuto O", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" } ] }, { "title": "Distinct tyrosine phosphorylation sites in ZAP-70 mediate activation and negative regulation of antigen receptor function.", "journal": "Molecular and cellular biology", "date": "1996", "authors": "Kong G, Dalton M, Bubeck Wardenburg J, Straus D, Kurosaki T, Chan AC", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ] } ], "crossref": [ { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SGLEPQPGVFDCLRDAMVRD", "down_seq": "VRQTWKLEGEALEQAIISQA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P43403-1", "kinase_gene_name": "ZAP70", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "10037717", "url": "https://glygen.org/publication/PubMed/10037717" }, { "database": "PubMed", "id": "8756661", "url": "https://glygen.org/publication/PubMed/8756661" } ], "site_lbl": "Tyr126" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ], "site_lbl": "Tyr126" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P43403-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43403-1.131.131", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43403-1.133.133", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43403-1.141.141", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43403-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43403-1.145.145", "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": 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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "Watts JD, Affolter M, Krebs DL, Wange RL, Samelson LE, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ] } ], "crossref": [ { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "HERMPWYHSSLTREEAERKL", "down_seq": "SGAQTDGKFLLRPRKEQGTY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06239-1", "kinase_gene_name": "LCK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ], "site_lbl": "Tyr178" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ], "site_lbl": "Tyr178" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43403-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43403-1.190.190", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43403-1.191.191", "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": "P43403-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "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": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KFDTLWQLVEYLKLKADGLI", "down_seq": "CLKEACPNSSASNASGAAAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "site_lbl": "Tyr248" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "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": "P43403-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "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": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] } ], "crossref": [ { "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLPAHPSTLTHPQRRIDTLN", "down_seq": "DGYTPEPARITSPDKPRPMP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" }, { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "site_lbl": "Ser289" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P43403-1.292.292", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43403-1.293.293", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43403-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43403-1.304.304", "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": "P43403-1.293.293", "start_pos": 293, "end_pos": 293, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "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": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] }, { "title": "Intensity and duration of TCR signaling is limited by p38 phosphorylation of ZAP-70(T293) and destabilization of the signalosome.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Giardino Torchia ML, Dutta D, Mittelstadt PR, Guha J, Gaida MM, Fish K, Barr VA, Akpan IO, Samelson LE, Tagad HD, Debnath S, Miller Jenkins LM, Appella E, Ashwell JD", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "29440413", "url": "https://glygen.org/publication/PubMed/29440413" } ] } ], "crossref": [ { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29440413", "url": "https://glygen.org/publication/PubMed/29440413", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HPSTLTHPQRRIDTLNSDGY", "down_seq": "PEPARITSPDKPRPMPMDTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" }, { "database": "PubMed", "id": "29440413", "url": "https://glygen.org/publication/PubMed/29440413" } ], "site_lbl": "Thr293" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P43403-1.289.289", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.292.292", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43403-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43403-1.304.304", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43403-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells.", "journal": "PloS one", "date": "2013", "authors": "Helou YA, Nguyen V, Beik SP, Salomon AR", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" } ] } ], "crossref": [ { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KADTEEMMREAQIMHQLDNP", "down_seq": "IVRLIGVCQAEALMLVMEMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" } ], "site_lbl": "Tyr397" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P43403-1.386.386", "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": "P43403-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "Watts JD, Affolter M, Krebs DL, Wange RL, Samelson LE, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ] }, { "title": "Tyrosine 474 of ZAP-70 is required for association with the Shc adaptor and for T-cell antigen receptor-dependent gene activation.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Pacini S, Ulivieri C, Di Somma MM, Isacchi A, Lanfrancone L, Pelicci PG, Telford JL, Baldari CT", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "9685404", "url": "https://glygen.org/publication/PubMed/9685404" } ] } ], "crossref": [ { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9685404", "url": "https://glygen.org/publication/PubMed/9685404", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EKNFVHRDLAARNVLLVNRH", "down_seq": "AKISDFGLSKALGADDSYYT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06239-1", "kinase_gene_name": "LCK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" }, { "database": "PubMed", "id": "9685404", "url": "https://glygen.org/publication/PubMed/9685404" } ], "site_lbl": "Tyr474" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P43403-1.461.461", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43403-1.465.465", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43403-1.479.479", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43403-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43403-1.492.492", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43403-1.493.493", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43403-1.494.494", "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": "P43403-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "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": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" }, { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] } ], "crossref": [ { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YAKISDFGLSKALGADDSYY", "down_seq": "ARSAGKWPLKWYAPECINFR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ], "site_lbl": "Thr494" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43403-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43403-1.479.479", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43403-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43403-1.492.492", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43403-1.493.493", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43403-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43403-1.497.497", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43403-1.514.514", "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": "P43403-1.520.520", "start_pos": 520, "end_pos": 520, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Critical role of Ser-520 phosphorylation for membrane recruitment and activation of the ZAP-70 tyrosine kinase in T cells.", "journal": "Molecular and cellular biology", "date": "2003", "authors": "Yang Y, Villain P, Mustelin T, Couture C", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "14560012", "url": "https://glygen.org/publication/PubMed/14560012" } ] } ], "crossref": [ { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "14560012", "url": "https://glygen.org/publication/PubMed/14560012", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KWPLKWYAPECINFRKFSSR", "down_seq": "DVWSYGVTMWEALSYGQKPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "14560012", "url": "https://glygen.org/publication/PubMed/14560012" } ], "site_lbl": "Ser520" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P43403-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43403-1.514.514", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43403-1.521.521", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43403-1.538.538", "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": "P43403-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P43403-1", "length": 619, "uniprot_id": "ZAP70_HUMAN", "protein_name": "Tyrosine-protein kinase ZAP-70", "refseq_ac": "NP_001070", "refseq_name": "tyrosine-protein kinase ZAP-70 isoform 1", "gene_name": "ZAP70", "gene_names_uniprotkb": "ZAP70; SRK", "gene_names_refseq": "ADMIO2; IMD48; SRK; STCD; STD; TZK; ZAP-70; ZAP70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43403", "url": "https://www.uniprot.org/uniprotkb/P43403" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification by electrospray ionization mass spectrometry of the sites of tyrosine phosphorylation induced in activated Jurkat T cells on the protein tyrosine kinase ZAP-70.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "Watts JD, Affolter M, Krebs DL, Wange RL, Samelson LE, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P43403-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403-1" } ], "reference": [ { "type": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ] }, { "title": "ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells.", "journal": "PloS one", "date": "2013", "authors": "Helou YA, Nguyen V, Beik SP, Salomon AR", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" } ], "reference": [ { "type": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" } ] } ], "crossref": [ { "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SLVHDVRFHHFPIERQLNGT", "down_seq": "AIAGGKAHCGPAELCEFYSR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06239-1", "kinase_gene_name": "LCK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ], "site_lbl": "Tyr69" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43403", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43403" }, { "database": "PubMed", "id": "23874979", "url": "https://glygen.org/publication/PubMed/23874979" }, { "database": "PubMed", "id": "7961936", "url": "https://glygen.org/publication/PubMed/7961936" } ], "site_lbl": "Tyr69" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "497", "end_pos": "497" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "315", "end_pos": "319" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "598", "end_pos": "598" } ] }, { "type": "snv", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P43403-1.70.70", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q969J2-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "Q969J2-1", "length": 545, "uniprot_id": "ZKSC4_HUMAN", "protein_name": "Zinc finger protein with KRAB and SCAN domains 4", "refseq_ac": "NP_061983", "refseq_name": "zinc finger protein with KRAB and SCAN domains 4 isoform 1", "gene_name": "ZKSCAN4", "gene_names_uniprotkb": "ZKSCAN4; ZNF307; ZNF427", "gene_names_refseq": "P1P373C6; ZKSCAN4; ZNF307; ZNF427; ZSCAN36", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q969J2", "url": "https://www.uniprot.org/uniprotkb/Q969J2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q969J2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q969J2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HGDKNVQNPEHGESWESQGR", "down_seq": "ESQWENTEAPVSYKCNECER", "snv": [ { "evidence": [ { "id": "Q969J2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q969J2" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "T", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "6", "chr_pos": "28245333", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T474", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "474", "end_pos": "474" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "165", "end_pos": "165" } ] } ], "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": "Q969J2-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q969J2-1", "length": 545, "uniprot_id": "ZKSC4_HUMAN", "protein_name": "Zinc finger protein with KRAB and SCAN domains 4", "refseq_ac": "NP_061983", "refseq_name": "zinc finger protein with KRAB and SCAN domains 4 isoform 1", "gene_name": "ZKSCAN4", "gene_names_uniprotkb": "ZKSCAN4; ZNF307; ZNF427", "gene_names_refseq": "P1P373C6; ZKSCAN4; ZNF307; ZNF427; ZSCAN36", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q969J2", "url": "https://www.uniprot.org/uniprotkb/Q969J2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q969J2", "url": "https://www.uniprot.org/uniprotkb/Q969J2" }, { "database": "iPTMnet", "id": "Q969J2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969J2" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] } ], "crossref": [ { "id": "Q969J2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969J2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GDQGQELLCCKMALLTQTQG", "down_seq": "QSSQCQPMKALFKHESLGSQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q969J2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969J2" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ], "site_lbl": "Ser165" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "474", "end_pos": "474" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "165", "end_pos": "165" } ] } ], "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": "Q6NZY7-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "Q6NZY7-1", "length": 148, "uniprot_id": "BORG3_HUMAN", "protein_name": "Cdc42 effector protein 5", "refseq_ac": "NP_659494", "refseq_name": "cdc42 effector protein 5", "gene_name": "CDC42EP5", "gene_names_uniprotkb": "CDC42EP5; BORG3; CEP5", "gene_names_refseq": "Borg3; CDC42EP5; CEP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZY7", "url": "https://www.uniprot.org/uniprotkb/Q6NZY7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZY7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZY7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SFHLDLGPSMLDAVLGVMDA", "down_seq": "RPEAAAAKPDAEPRPGTQPP", "snv": [ { "evidence": [ { "id": "Q6NZY7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZY7" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "19", "chr_pos": "54465219", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A110", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "126", "end_pos": "126" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q6NZY7-1.126.126", "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": "Q6NZY7-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "Q6NZY7-1", "length": 148, "uniprot_id": "BORG3_HUMAN", "protein_name": "Cdc42 effector protein 5", "refseq_ac": "NP_659494", "refseq_name": "cdc42 effector protein 5", "gene_name": "CDC42EP5", "gene_names_uniprotkb": "CDC42EP5; BORG3; CEP5", "gene_names_refseq": "Borg3; CDC42EP5; CEP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZY7", "url": "https://www.uniprot.org/uniprotkb/Q6NZY7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZY7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZY7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VMDAARPEAAAAKPDAEPRP", "down_seq": "TQPPQARCRPNADLELNDVI", "snv": [ { "evidence": [ { "id": "Q6NZY7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZY7" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "54465172", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G126", "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:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "126", "end_pos": "126" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6NZY7-1.110.110", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H6E4-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "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": "Positive selection CRISPR screens reveal a druggable pocket in an oligosaccharyltransferase required for inflammatory signaling to NF-\u03baB.", "journal": "Cell", "date": "2024-04-25", "authors": "Lampson Benjamin L, Ram\u03afrez Ana S, Baro Marta, He Lixia, Hegde Mudra, Koduri Vidyasagar, Pfaff Jamie L, Hanna Ruth E, Kowal Julia, Shirole Nitin H, He Yanfeng, Doench John G, Contessa Joseph N, Locher Kaspar P, Kaelin William G", "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4#ptm_processing" }, { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "reference": [ { "type": "PubMed", "id": "38670073", "url": "https://glygen.org/publication/PubMed/38670073" } ] } ], "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": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38670073", "url": "https://glygen.org/publication/PubMed/38670073", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1458263140", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1458263140", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1458263140", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1458263140", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YYFDHNSNWNLLIRWGISFC", "down_seq": "QTGVFNQGPHSPILSLMAQE", "glycosylation": [ { "glytoucan_ac": "G65000LJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "WGISFCNQTGVFNQGPHSPILSLMAQELGISEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn148", "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": "Asn148", "evidence": [ { "id": "Q9H6E4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4#ptm_processing" }, { "id": "38670073", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38670073" } ] } ], "snv": [ { "evidence": [ { "id": "rs1458263140", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1458263140" }, { "id": "rs1458263140", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1458263140" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQT->SQT).", "chr_id": "22", "chr_pos": "41813396", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N148", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9H6E4-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9H6E4-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9H6E4-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9H6E4-1.150.150", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H6E4-1.184.198", "start_pos": 184, "end_pos": 198, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "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": "IDRTEFIPSTDPFQK", "start_aa": "I", "up_seq": "LMAQELGISEKDSNFQNPFK", "down_seq": "ALREEEKRRKKEEKRKEIRK", "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": "IDRTEFIPSTDPFQK", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ile", "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": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9H6E4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9H6E4-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9H6E4-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9H6E4-1.190.200", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9H6E4-1.192.192", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9H6E4-1.192.193", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9H6E4-1.193.193", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9H6E4-1.217.217", "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": "Q9H6E4-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "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" } ] }, { "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": "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": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs201507268", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201507268", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201507268", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201507268", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201507268", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201507268", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201507268", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201507268#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201507268", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201507268", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QELGISEKDSNFQNPFKIDR", "down_seq": "EFIPSTDPFQKALREEEKRR", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr187", "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" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "snv": [ { "evidence": [ { "id": "rs201507268", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201507268" }, { "id": "rs201507268", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201507268" }, { "id": "rs201507268", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201507268" }, { "id": "rs201507268", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201507268#frequency_tab" }, { "id": "rs201507268", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201507268" } ], "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": "22", "chr_pos": "41813818", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T187", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201507268", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201507268" }, { "id": "rs201507268", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201507268" }, { "id": "rs201507268", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201507268" }, { "id": "rs201507268", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201507268#frequency_tab" }, { "id": "rs201507268", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201507268" } ], "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": "22", "chr_pos": "41813818", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T187", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9H6E4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9H6E4-1.184.198", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9H6E4-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9H6E4-1.190.200", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9H6E4-1.192.192", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9H6E4-1.192.193", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9H6E4-1.193.193", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H6E4-1.190.200", "start_pos": 190, "end_pos": 200, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "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": "IPSTDPFQKAL", "start_aa": "I", "up_seq": "GISEKDSNFQNPFKIDRTEF", "down_seq": "REEEKRRKKEEKRKEIRKGP", "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": "IPSTDPFQKAL", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ile", "end_aa": "Leu", "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": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9H6E4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9H6E4-1.184.198", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9H6E4-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9H6E4-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9H6E4-1.192.192", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9H6E4-1.192.193", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9H6E4-1.193.193", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9H6E4-1.217.217", "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": "Q9H6E4-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "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" } ] }, { "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" } ] }, { "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": "Q9H6E4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H6E4" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "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": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs1226622265", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226622265", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1226622265", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1226622265", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9H6E4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H6E4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1284520804", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284520804", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1284520804", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1284520804#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1284520804", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1284520804", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9H6E4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H6E4", "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": "SEKDSNFQNPFKIDRTEFIP", "down_seq": "TDPFQKALREEEKRRKKEEK", "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": "Ser192", "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" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "snv": [ { "evidence": [ { "id": "rs1226622265", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226622265" }, { "id": "rs1226622265", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1226622265" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->G).", "chr_id": "22", "chr_pos": "41825707", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S192", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9H6E4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H6E4" }, { "id": "rs1284520804", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284520804" }, { "id": "rs1284520804", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1284520804#frequency_tab" }, { "id": "rs1284520804", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1284520804" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->N).", "chr_id": "22", "chr_pos": "41825708", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S192", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H6E4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H6E4" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser192" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9H6E4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9H6E4-1.184.198", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9H6E4-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9H6E4-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9H6E4-1.190.200", "categories": [ "glycosylation_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q9H6E4-1.192.193", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9H6E4-1.193.193", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "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": 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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H6E4-1.192.193", "start_pos": 192, "end_pos": 193, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "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": "ST", "start_aa": "S", "up_seq": "SEKDSNFQNPFKIDRTEFIP", "down_seq": "DPFQKALREEEKRRKKEEKR", "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": "ST", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Thr", "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": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9H6E4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9H6E4-1.184.198", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9H6E4-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9H6E4-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9H6E4-1.190.200", "categories": [ "glycosylation_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q9H6E4-1.192.192", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q9H6E4-1.193.193", "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" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 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": "Q9H6E4-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "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" } ] }, { "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": "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": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs61109016", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61109016", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61109016", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61109016", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61109016", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61109016", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61109016", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61109016#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61109016", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61109016", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EKDSNFQNPFKIDRTEFIPS", "down_seq": "DPFQKALREEEKRRKKEEKR", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr193", "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" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "snv": [ { "evidence": [ { "id": "rs61109016", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61109016" }, { "id": "rs61109016", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61109016" }, { "id": "rs61109016", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61109016" }, { "id": "rs61109016", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61109016#frequency_tab" }, { "id": "rs61109016", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61109016" } ], "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": "22", "chr_pos": "41825710", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.0105965", "site_lbl": "T193", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9H6E4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9H6E4-1.184.198", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9H6E4-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9H6E4-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9H6E4-1.190.200", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9H6E4-1.192.192", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q9H6E4-1.192.193", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q9H6E4-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "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": "Q9H6E4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H6E4" } ], "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": "Q9H6E4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H6E4", "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": "Q9H6E4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H6E4" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "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": "Q9H6E4-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Regulated N-glycosylation controls chaperone function and receptor trafficking.", "journal": "Science (New York, N.Y.)", "date": "2024-11-08", "authors": "Ma Mengxiao, Dubey Ramin, Jen Annie, Pusapati Ganesh V, Singal Bharti, Shishkova Evgenia, Overmyer Katherine A, Cormier-Daire Val\u00e9rie, Fedry Juliette, Aravind L, Coon Joshua J, Rohatgi Rajat", "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "reference": [ { "type": "PubMed", "id": "39509507", "url": "https://glygen.org/publication/PubMed/39509507" } ] } ], "crossref": [ { "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "39509507", "url": "https://glygen.org/publication/PubMed/39509507", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KEEKRKEIRKGPRISRSQSE", "down_seq": "", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "Abolished retention in the endoplasmic reticulum leading to secretion.", "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" }, { "database": "PubMed", "id": "39509507", "url": "https://glygen.org/publication/PubMed/39509507" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9H6E4-1.217.217", "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": "Q9H6E4-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768445622", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768445622", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768445622", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768445622", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768445622", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768445622#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768445622", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768445622", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9H6E4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H6E4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GPFPQDEKLKDAFSHVVENT", "down_seq": "FFGDVVLRFPRIVHYYFDHN", "snv": [ { "evidence": [ { "id": "rs768445622", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768445622" }, { "id": "rs768445622", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768445622" }, { "id": "rs768445622", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768445622#frequency_tab" }, { "id": "rs768445622", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768445622" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTS).", "chr_id": "22", "chr_pos": "41813290", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A113", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9H6E4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H6E4" } ], "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": "22", "chr_pos": "41813290", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A113", "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": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "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", "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": "Q9H6E4-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs531928294", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs531928294", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs531928294", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs531928294", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs531928294", "url": "https://www.ncbi.nlm.nih.gov/snp/rs531928294#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs531928294", "url": "http://gnomad.broadinstitute.org/awesome?query=rs531928294", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FGDVVLRFPRIVHYYFDHNS", "down_seq": "WNLLIRWGISFCNQTGVFNQ", "snv": [ { "evidence": [ { "id": "rs531928294", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs531928294" }, { "id": "rs531928294", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs531928294" }, { "id": "rs531928294", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs531928294#frequency_tab" }, { "id": "rs531928294", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs531928294" } ], "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": "22", "chr_pos": "41813357", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N135", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs531928294", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs531928294" }, { "id": "rs531928294", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs531928294" }, { "id": "rs531928294", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs531928294#frequency_tab" }, { "id": "rs531928294", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs531928294" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSN->NST).", "chr_id": "22", "chr_pos": "41813357", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N135", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H6E4-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9H6E4-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9H6E4-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9H6E4-1.150.150", "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" ] }, { "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": "Q9H6E4-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1291707382", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1291707382", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1291707382", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1291707382", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DVVLRFPRIVHYYFDHNSNW", "down_seq": "LLIRWGISFCNQTGVFNQGP", "snv": [ { "evidence": [ { "id": "rs1291707382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1291707382" }, { "id": "rs1291707382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1291707382" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NWN->NWT).", "chr_id": "22", "chr_pos": "41813363", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N137", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H6E4-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9H6E4-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9H6E4-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9H6E4-1.150.150", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H6E4-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767967796", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767967796", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767967796", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767967796", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767967796", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767967796", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "YFDHNSNWNLLIRWGISFCN", "down_seq": "TGVFNQGPHSPILSLMAQEL", "snv": [ { "evidence": [ { "id": "rs767967796", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767967796" }, { "id": "rs767967796", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767967796" }, { "id": "rs767967796", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767967796" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "Q", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQT->NPT).", "chr_id": "22", "chr_pos": "41813399", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q149", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9H6E4-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9H6E4-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9H6E4-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9H6E4-1.150.150", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H6E4-1.150.150", "start_pos": 150, "end_pos": 150, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753141912", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753141912", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753141912", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753141912", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FDHNSNWNLLIRWGISFCNQ", "down_seq": "GVFNQGPHSPILSLMAQELG", "snv": [ { "evidence": [ { "id": "rs753141912", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753141912" }, { "id": "rs753141912", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753141912" } ], "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 (NQT->NQI).", "chr_id": "22", "chr_pos": "41813402", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T150", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9H6E4-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9H6E4-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9H6E4-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9H6E4-1.149.149", "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": "Q9H6E4-1.174.174", "start_pos": 174, "end_pos": 174, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2076609505", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2076609505", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2076609505", "url": "https://www.ensembl.org/id/rs2076609505", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NQGPHSPILSLMAQELGISE", "down_seq": "DSNFQNPFKIDRTEFIPSTD", "snv": [ { "evidence": [ { "id": "rs2076609505", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2076609505" }, { "id": "rs2076609505", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2076609505" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KDS->NDS).", "chr_id": "22", "chr_pos": "41813780", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K174", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q9H6E4-1.184.198", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9H6E4-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9H6E4-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9H6E4-1.190.200", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9H6E4-1.192.192", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9H6E4-1.192.193", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9H6E4-1.193.193", "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": "Q9H6E4-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777145752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777145752", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777145752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777145752", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777145752", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777145752#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777145752", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777145752", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MAQELGISEKDSNFQNPFKI", "down_seq": "RTEFIPSTDPFQKALREEEK", "snv": [ { "evidence": [ { "id": "rs777145752", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777145752" }, { "id": "rs777145752", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777145752" }, { "id": "rs777145752", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777145752#frequency_tab" }, { "id": "rs777145752", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777145752" } ], "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": "22", "chr_pos": "41813811", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D185", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9H6E4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9H6E4-1.184.198", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9H6E4-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9H6E4-1.190.200", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9H6E4-1.192.192", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9H6E4-1.192.193", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9H6E4-1.193.193", "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": "Q9H6E4-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H6E4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H6E4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QKALREEEKRRKKEEKRKEI", "down_seq": "KGPRISRSQSEL", "snv": [ { "evidence": [ { "id": "Q9H6E4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H6E4" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "41825783", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R217", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9H6E4-1.184.198", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9H6E4-1.190.200", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9H6E4-1.229.229", "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": "Q9H6E4-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "Q9H6E4-1", "length": 229, "uniprot_id": "CC134_HUMAN", "protein_name": "Coiled-coil domain-containing protein 134", "refseq_ac": "NP_079097", "refseq_name": "coiled-coil domain-containing protein 134 isoform 1 precursor", "gene_name": "CCDC134", "gene_names_uniprotkb": "CCDC134", "gene_names_refseq": "CCDC134; OI22", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H6E4", "url": "https://www.uniprot.org/uniprotkb/Q9H6E4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H6E4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H6E4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "FEVKRREQLLALKNLAQLND", "down_seq": "HQQYKILDVMLKGLFKVLED", "snv": [ { "evidence": [ { "id": "Q9H6E4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H6E4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "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": "22", "chr_pos": "41809951", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "I59", "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": "148", "end_pos": "148" }, { "start_pos": "184", "end_pos": "198" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "200" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "192", "end_pos": "193" }, { "start_pos": "193", "end_pos": "193" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "192", "end_pos": "192" } ] } ], "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": "P21730-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2122141818", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122141818", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2122141818", "url": "https://www.ensembl.org/id/rs2122141818", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1273808323", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1273808323", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1273808323", "url": "https://www.ensembl.org/id/rs1273808323", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MDSF", "down_seq": "YTTPDYGHYDDKDTLDLNTP", "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": "Asn5", "evidence": [ { "id": "P21730", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P21730#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2122141818", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122141818" }, { "id": "rs2122141818", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2122141818" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NYT->DYT).", "chr_id": "19", "chr_pos": "47319790", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N5", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1273808323", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1273808323" }, { "id": "rs1273808323", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1273808323" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NYT->SYT).", "chr_id": "19", "chr_pos": "47319791", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N5", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P21730-1.25.25", "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": 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" ] }, { "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": "P21730-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "DeMartino JA, Van Riper G, Siciliano SJ, Molineaux CJ, Konteatis ZD, Rosen H, Springer MS", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] }, { "title": "Residues 10-18 within the C5a receptor N terminus compose a binding domain for chemotaxis inhibitory protein of Staphylococcus aureus.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Postma B, Kleibeuker W, Poppelier MJ, Boonstra M, Van Kessel KP, Van Strijp JA, de Haas CJ", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MDSFNYTTP", "down_seq": "YGHYDDKDTLDLNTPVDKTS", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Strongly impairs C5a binding; when associated with A-15; A-16; A-18 and A-21 (PubMed:8182049). Moderately impairs CHIPS binding (PubMed:15542591). Strongly impairs CHIPS binding; when associated with A-15 (PubMed:15542591). Strongly impairs CHIPS binding; when associated with A-18 (PubMed:15542591).", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" }, { "database": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.28.28", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P21730-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Tyrosine sulfation in N-terminal domain of human C5a receptor is necessary for binding of chemotaxis inhibitory protein of Staphylococcus aureus.", "journal": "Acta pharmacologica Sinica", "date": "2011", "authors": "Liu ZJ, Yang YJ, Jiang L, Xu YC, Wang AX, Du GH, Gao JM", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "21706042", "url": "https://glygen.org/publication/PubMed/21706042" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21706042", "url": "https://glygen.org/publication/PubMed/21706042", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MDSFNYTTPD", "down_seq": "GHYDDKDTLDLNTPVDKTSN", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Weakly impairs CHIPS binding. Loss of CHIPS binding; when associated with F-14.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "21706042", "url": "https://glygen.org/publication/PubMed/21706042" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P21730-1.28.28", "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": "P21730-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Residues 10-18 within the C5a receptor N terminus compose a binding domain for chemotaxis inhibitory protein of Staphylococcus aureus.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Postma B, Kleibeuker W, Poppelier MJ, Boonstra M, Van Kessel KP, Van Strijp JA, de Haas CJ", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MDSFNYTTPDY", "down_seq": "HYDDKDTLDLNTPVDKTSNT", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "A", "comment": "Moderately impairs CHIPS binding.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.28.28", "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": "P21730-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "C5a receptor oligomerization. I. Disulfide trapping reveals oligomers and potential contact surfaces in a G protein-coupled receptor.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Klco JM, Lassere TB, Baranski TJ", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "ILLLATISADRFLLVFKPIW", "down_seq": "QNFRGAGLAWIACAVAWGLA", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "Fails to homodimerize.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P21730-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.157.157", "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": "P21730-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Tyrosine sulfation in N-terminal domain of human C5a receptor is necessary for binding of chemotaxis inhibitory protein of Staphylococcus aureus.", "journal": "Acta pharmacologica Sinica", "date": "2011", "authors": "Liu ZJ, Yang YJ, Jiang L, Xu YC, Wang AX, Du GH, Gao JM", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "21706042", "url": "https://glygen.org/publication/PubMed/21706042" } ] }, { "title": "Residues 10-18 within the C5a receptor N terminus compose a binding domain for chemotaxis inhibitory protein of Staphylococcus aureus.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Postma B, Kleibeuker W, Poppelier MJ, Boonstra M, Van Kessel KP, Van Strijp JA, de Haas CJ", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21706042", "url": "https://glygen.org/publication/PubMed/21706042", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MDSFNYTTPDYGH", "down_seq": "DDKDTLDLNTPVDKTSNTLR", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Weakly impairs CHIPS binding (PubMed:15542591). Strongly impairs CHIPS binding (PubMed:21706042). Loss of CHIPS binding; when associated with F-11 (PubMed:21706042).", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "21706042", "url": "https://glygen.org/publication/PubMed/21706042" }, { "database": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P21730-1.34.34", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P21730-1.157.157", "start_pos": 157, "end_pos": 157, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "C5a receptor oligomerization. I. Disulfide trapping reveals oligomers and potential contact surfaces in a G protein-coupled receptor.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Klco JM, Lassere TB, Baranski TJ", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "LVFKPIWCQNFRGAGLAWIA", "down_seq": "AVAWGLALLLTIPSFLYRVV", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "No effect on homodimer formation.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P21730-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.175.175", "categories": [ "mutagenesis_flag", "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": "P21730-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "DeMartino JA, Van Riper G, Siciliano SJ, Molineaux CJ, Konteatis ZD, Rosen H, Springer MS", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] }, { "title": "Residues 10-18 within the C5a receptor N terminus compose a binding domain for chemotaxis inhibitory protein of Staphylococcus aureus.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Postma B, Kleibeuker W, Poppelier MJ, Boonstra M, Van Kessel KP, Van Strijp JA, de Haas CJ", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MDSFNYTTPDYGHY", "down_seq": "DKDTLDLNTPVDKTSNTLRV", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Strongly impairs C5a binding; when associated with A-10; A-16; A-18 and A-21 (PubMed:8182049). Moderately impairs CHIPS binding (PubMed:15542591). Strongly impairs CHIPS binding; when associated with A-10 (PubMed:15542591). Strongly impairs CHIPS binding; when associated with A-18 (PubMed:15542591).", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" }, { "database": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P21730-1.34.34", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P21730-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "DeMartino JA, Van Riper G, Siciliano SJ, Molineaux CJ, Konteatis ZD, Rosen H, Springer MS", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MDSFNYTTPDYGHYD", "down_seq": "KDTLDLNTPVDKTSNTLRVP", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Strongly impairs C5a binding; when associated with A-10; A-15; A-18 and A-21.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.34.34", "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": "P21730-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IACAVAWGLALLLTIPSFLY", "down_seq": "VVREEYFPPKVLCGVDYSHD", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Reduced activation by anaphylatoxin C5a.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "47320300", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R175", "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: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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P21730-1.157.157", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.180.180", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.182.182", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.191.191", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P21730-1.195.195", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "P21730-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AWGLALLLTIPSFLYRVVRE", "down_seq": "YFPPKVLCGVDYSHDKRRER", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Decreased ability to activate G(i)/GNAI1.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P21730-1.175.175", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.182.182", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.191.191", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P21730-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P21730-1.199.199", "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": "P21730-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "WGLALLLTIPSFLYRVVREE", "down_seq": "FPPKVLCGVDYSHDKRRERA", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Decreased ability to activate G(i)/GNAI1.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P21730-1.175.175", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.180.180", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.182.182", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.191.191", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P21730-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.199.199", "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": "P21730-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "GLALLLTIPSFLYRVVREEY", "down_seq": "PPKVLCGVDYSHDKRRERAV", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "Decreased ability to activate G(i)/GNAI1.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P21730-1.175.175", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.180.180", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.191.191", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P21730-1.199.199", "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": "P21730-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LALLLTIPSFLYRVVREEYF", "down_seq": "PKVLCGVDYSHDKRRERAVA", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "Decreased ability to activate G(i)/GNAI1.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P21730-1.175.175", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.180.180", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.182.182", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.191.191", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.199.199", "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": "P21730-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "DeMartino JA, Van Riper G, Siciliano SJ, Molineaux CJ, Konteatis ZD, Rosen H, Springer MS", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] }, { "title": "Residues 10-18 within the C5a receptor N terminus compose a binding domain for chemotaxis inhibitory protein of Staphylococcus aureus.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Postma B, Kleibeuker W, Poppelier MJ, Boonstra M, Van Kessel KP, Van Strijp JA, de Haas CJ", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MDSFNYTTPDYGHYDDK", "down_seq": "TLDLNTPVDKTSNTLRVPDI", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Strongly impairs C5a binding; when associated with A-10; A-15; A-16 and A-21 (PubMed:8182049). Impairs CHIPS binding (PubMed:15542591). Strongly impairs CHIPS binding; when associated with A-10 (PubMed:15542591). Strongly impairs CHIPS binding; when associated with A-15 (PubMed:15542591).", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" }, { "database": "PubMed", "id": "15542591", "url": "https://glygen.org/publication/PubMed/15542591" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.34.34", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P21730-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1407617126", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1407617126", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1407617126", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1407617126", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SFLYRVVREEYFPPKVLCGV", "down_seq": "YSHDKRRERAVAIVRLVLGF", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Reduced activation by anaphylatoxin C5a.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" }, { "id": "rs1407617126", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1407617126" }, { "id": "rs1407617126", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1407617126" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DYS->NYS).", "chr_id": "19", "chr_pos": "47320348", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D191", "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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P21730-1.175.175", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P21730-1.180.180", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P21730-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.182.182", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P21730-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.199.199", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "P21730-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] }, { "title": "Mutation of glutamate 199 of the human C5a receptor defines a binding site for ligand distinct from the receptor N terminus.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Monk PN, Barker MD, Partridge LJ, Pease JE", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "7622471", "url": "https://glygen.org/publication/PubMed/7622471" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7622471", "url": "https://glygen.org/publication/PubMed/7622471", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "EEYFPPKVLCGVDYSHDKRR", "down_seq": "RAVAIVRLVLGFLWPLLTLT", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Reduced activation by anaphylatoxin C5a.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] }, { "sequence_org": "E", "sequence_mut": "Q", "comment": "Impairs C5a binding (10-fold reduction) and C5a-induced 5-HT secretion.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "7622471", "url": "https://glygen.org/publication/PubMed/7622471" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P21730-1.180.180", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P21730-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P21730-1.182.182", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P21730-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P21730-1.191.191", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.195.195", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P21730-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "DeMartino JA, Van Riper G, Siciliano SJ, Molineaux CJ, Konteatis ZD, Rosen H, Springer MS", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MDSFNYTTPDYGHYDDKDTL", "down_seq": "LNTPVDKTSNTLRVPDILAL", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Strongly impairs C5a binding; when associated with A-10; A-15; A-16 and A-18.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.34.34", "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": "P21730-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "C5a receptor oligomerization. I. Disulfide trapping reveals oligomers and potential contact surfaces in a G protein-coupled receptor.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Klco JM, Lassere TB, Baranski TJ", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "AVAIVRLVLGFLWPLLTLTI", "down_seq": "YTFILLRTWSRRATRSTKTL", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "No effect on homodimer formation.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "12835319", "url": "https://glygen.org/publication/PubMed/12835319" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P21730-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.239.239", "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": "P21730-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Revealing the signaling of complement receptors C3aR and C5aR1 by anaphylatoxins.", "journal": "Nature chemical biology", "date": "2023-11", "authors": "Wang Yue, Liu Weiyi, Xu Youwei, He Xinheng, Yuan Qingning, Luo Ping, Fan Wenjia, Zhu Jingpeng, Zhang Xinyue, Cheng Xi, Jiang Yi, Xu H Eric, Zhuang Youwen", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" } ] }, { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TKTLKVVVAVVASFFIFWLP", "down_seq": "QVTGIMMSFLEPSSPTFLLL", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Decreased ability to activate G(i)/GNAI1. Reduced activation by anaphylatoxin C5a.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P21730-1.239.239", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P21730-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "DeMartino JA, Van Riper G, Siciliano SJ, Molineaux CJ, Konteatis ZD, Rosen H, Springer MS", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] }, { "title": "Revealing the signaling of complement receptors C3aR and C5aR1 by anaphylatoxins.", "journal": "Nature chemical biology", "date": "2023-11", "authors": "Wang Yue, Liu Weiyi, Xu Youwei, He Xinheng, Yuan Qingning, Luo Ping, Fan Wenjia, Zhu Jingpeng, Zhang Xinyue, Cheng Xi, Jiang Yi, Xu H Eric, Zhuang Youwen", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs769494579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769494579", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769494579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769494579", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769494579", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769494579#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769494579", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769494579", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TTPDYGHYDDKDTLDLNTPV", "down_seq": "KTSNTLRVPDILALVIFAVV", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Strongly impairs C5a binding; when associated with 2-D--L-22 Del. Decreased ability to activate G(i)/GNAI1.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" }, { "database": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" } ] } ], "snv": [ { "evidence": [ { "id": "rs769494579", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769494579" }, { "id": "rs769494579", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769494579" }, { "id": "rs769494579", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769494579#frequency_tab" }, { "id": "rs769494579", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769494579" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DKT->NKT).", "chr_id": "19", "chr_pos": "47319856", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D27", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.34.34", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P21730-1.282.282", "start_pos": 282, "end_pos": 282, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Revealing the signaling of complement receptors C3aR and C5aR1 by anaphylatoxins.", "journal": "Nature chemical biology", "date": "2023-11", "authors": "Wang Yue, Liu Weiyi, Xu Youwei, He Xinheng, Yuan Qingning, Luo Ping, Fan Wenjia, Zhu Jingpeng, Zhang Xinyue, Cheng Xi, Jiang Yi, Xu H Eric, Zhuang Youwen", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" } ] }, { "title": "Mechanism of activation and biased signaling in complement receptor C5aR1.", "journal": "Cell research", "date": "2023-04", "authors": "Feng Yuying, Zhao Chang, Deng Yue, Wang Heli, Ma Liang, Liu Sicen, Tian Xiaowen, Wang Bo, Bin Yan, Chen Peipei, Yan Wei, Fu Ping, Shao Zhenhua", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GIMMSFLEPSSPTFLLLKKL", "down_seq": "SLCVSFAYINCCINPIIYVV", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Decreased ability to activate G(i)/GNAI1. Reduced activation by anaphylatoxin C5a.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" }, { "database": "PubMed", "id": "36806352", "url": "https://glygen.org/publication/PubMed/36806352" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "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": "P21730-1.2.22", "start_pos": 2, "end_pos": 22, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "DeMartino JA, Van Riper G, Siciliano SJ, Molineaux CJ, Konteatis ZD, Rosen H, Springer MS", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DSFNYTTPDYGHYDDKDTLDL", "start_aa": "D", "up_seq": "M", "down_seq": "NTPVDKTSNTLRVPDILALV", "mutagenesis": [ { "sequence_org": "DSFNYTTPDYGHYDDKDTLDL", "sequence_mut": "", "comment": "Impairs C5a binding. Strongly impairs C5a binding; when associated with A-27.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.34.34", "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": "P21730-1.2.30", "start_pos": 2, "end_pos": 30, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs.", "journal": "The Journal of biological chemistry", "date": "1994", "authors": "DeMartino JA, Van Riper G, Siciliano SJ, Molineaux CJ, Konteatis ZD, Rosen H, Springer MS", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DSFNYTTPDYGHYDDKDTLDLNTPVDKTS", "start_aa": "D", "up_seq": "M", "down_seq": "NTLRVPDILALVIFAVVFLV", "mutagenesis": [ { "sequence_org": "DSFNYTTPDYGHYDDKDTLDLNTPVDKTS", "sequence_mut": "", "comment": "Strongly impairs C5a binding (45,000-fold).", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "8182049", "url": "https://glygen.org/publication/PubMed/8182049" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.34.34", "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": "P21730-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural snapshots uncover a key phosphorylation motif in GPCRs driving \u03b2-arrestin activation.", "journal": "Molecular cell", "date": "2023-06-15", "authors": "Maharana Jagannath, Sarma Parishmita, Yadav Manish K, Saha Sayantan, Singh Vinay, Saha Shirsha, Chami Mohamed, Banerjee Ramanuj, Shukla Arun K", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSLLRNVLTEESVVRESKSF", "down_seq": "RSTVDTMAQKTQAV", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "TR", "comment": "Impaired interaction with ARRB1 and ARRB2.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686" } ], "site_lbl": "Thr336" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P21730-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.334.334", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.338.338", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.339.339", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.342.342", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": "P21730-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Revealing the signaling of complement receptors C3aR and C5aR1 by anaphylatoxins.", "journal": "Nature chemical biology", "date": "2023-11", "authors": "Wang Yue, Liu Weiyi, Xu Youwei, He Xinheng, Yuan Qingning, Luo Ping, Fan Wenjia, Zhu Jingpeng, Zhang Xinyue, Cheng Xi, Jiang Yi, Xu H Eric, Zhuang Youwen", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "HYDDKDTLDLNTPVDKTSNT", "down_seq": "RVPDILALVIFAVVFLVGVL", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "", "comment": "Decreased ability to activate G(i)/GNAI1.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.34.34", "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": "P21730-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Revealing the signaling of complement receptors C3aR and C5aR1 by anaphylatoxins.", "journal": "Nature chemical biology", "date": "2023-11", "authors": "Wang Yue, Liu Weiyi, Xu Youwei, He Xinheng, Yuan Qingning, Luo Ping, Fan Wenjia, Zhu Jingpeng, Zhang Xinyue, Cheng Xi, Jiang Yi, Xu H Eric, Zhuang Youwen", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YDDKDTLDLNTPVDKTSNTL", "down_seq": "VPDILALVIFAVVFLVGVLG", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "", "comment": "Decreased ability to activate G(i)/GNAI1.", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "37169960", "url": "https://glygen.org/publication/PubMed/37169960" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.33.33", "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": "P21730-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2122142696", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122142696", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2122142696", "url": "https://www.ensembl.org/id/rs2122142696", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "HWPFGGAACSILPSLILLNM", "down_seq": "ASILLLATISADRFLLVFKP", "snv": [ { "evidence": [ { "id": "rs2122142696", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122142696" }, { "id": "rs2122142696", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2122142696" } ], "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 (NMY->NMC).", "chr_id": "19", "chr_pos": "47320139", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y121", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P21730-1.132.132", "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": "P21730-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LPSLILLNMYASILLLATIS", "down_seq": "DRFLLVFKPIWCQNFRGAGL", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "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": "19", "chr_pos": "47320171", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A132", "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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P21730-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.148.148", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P21730-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ATISADRFLLVFKPIWCQNF", "down_seq": "GAGLAWIACAVAWGLALLLT", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "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 (4).", "chr_id": "19", "chr_pos": "47320220", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R148", "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: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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P21730-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.144.144", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.157.157", "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": "P21730-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MDSFNYTTPDYGHYDD", "down_seq": "DTLDLNTPVDKTSNTLRVPD", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KDT->NDT).", "chr_id": "19", "chr_pos": "47319828", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K17", "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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P21730-1.34.34", "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": "P21730-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RVVREEYFPPKVLCGVDYSH", "down_seq": "KRRERAVAIVRLVLGFLWPL", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "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": "19", "chr_pos": "47320360", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D195", "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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P21730-1.175.175", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P21730-1.180.180", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P21730-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P21730-1.182.182", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P21730-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.191.191", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.199.199", "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": "P21730-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VLGFLWPLLTLTICYTFILL", "down_seq": "TWSRRATRSTKTLKVVVAVV", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "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": "19", "chr_pos": "47320459", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R228", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P21730-1.221.221", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.239.239", "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": "P21730-1.239.239", "start_pos": 239, "end_pos": 239, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TICYTFILLRTWSRRATRST", "down_seq": "TLKVVVAVVASFFIFWLPYQ", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "47320494", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K239", "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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P21730-1.221.221", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P21730-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P21730-1.258.258", "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": "P21730-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747815770", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747815770", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747815770", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747815770", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747815770", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747815770#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747815770", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747815770", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NYTTPDYGHYDDKDTLDLNT", "down_seq": "VDKTSNTLRVPDILALVIFA", "snv": [ { "evidence": [ { "id": "rs747815770", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747815770" }, { "id": "rs747815770", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747815770" }, { "id": "rs747815770", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747815770#frequency_tab" }, { "id": "rs747815770", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747815770" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTP->NTS).", "chr_id": "19", "chr_pos": "47319850", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P25", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "downstream", "id": "P21730-1.5.5", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.34.34", "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": "P21730-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TPDYGHYDDKDTLDLNTPVD", "down_seq": "TSNTLRVPDILALVIFAVVF", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "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": "19", "chr_pos": "47319861", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K28", "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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P21730-1.2.22", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.2.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P21730-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P21730-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P21730-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P21730-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P21730-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P21730-1.16.16", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P21730-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P21730-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.21.21", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.27.27", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.34.34", "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": "P21730-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LCVSFAYINCCINPIIYVVA", "down_seq": "QGFQGRLRKSLPSLLRNVLT", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "47320687", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G304", "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: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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P21730-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.314.314", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P21730-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NCCINPIIYVVAGQGFQGRL", "down_seq": "KSLPSLLRNVLTEESVVRES", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "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 (3).", "chr_id": "19", "chr_pos": "47320711", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R312", "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: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": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P21730-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.314.314", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P21730-1.332.332", "categories": [ "snv_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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P21730-1.320.320", "start_pos": 320, "end_pos": 320, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P21730", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YVVAGQGFQGRLRKSLPSLL", "down_seq": "NVLTEESVVRESKSFTRSTV", "snv": [ { "evidence": [ { "id": "P21730", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P21730" } ], "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 (4).", "chr_id": "19", "chr_pos": "47320736", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R320", "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": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P21730-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P21730-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.314.314", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P21730-1.334.334", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P21730-1.336.336", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.338.338", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P21730-1.339.339", "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": "P21730-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human complement 5a (C5a) anaphylatoxin receptor (CD88) phosphorylation sites and their specific role in receptor phosphorylation and attenuation of G protein-mediated responses. Desensitization of C5a receptor controls superoxide production but not receptor sequestration in HL-60 cells.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Christophe T, Rabiet MJ, Tardif M, Milcent MD, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" } ] }, { "title": "Identification of the major phosphorylation sites in human C5a anaphylatoxin receptor in vivo.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Giannini E, Brouchon L, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" } ] } ], "crossref": [ { "id": "rs1296732030", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1296732030", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1296732030", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1296732030", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKSLPSLLRNVLTEESVVRE", "down_seq": "KSFTRSTVDTMAQKTQAV", "snv": [ { "evidence": [ { "id": "rs1296732030", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1296732030" }, { "id": "rs1296732030", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1296732030" } ], "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": "19", "chr_pos": "47320772", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S332", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" }, { "database": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "site_lbl": "Ser332" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P21730-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P21730-1.314.314", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P21730-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.334.334", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.336.336", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.338.338", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.339.339", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.342.342", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P21730-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2059303114", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2059303114", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2059303114", "url": "https://www.ensembl.org/id/rs2059303114", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VFLVGVLGNALVVWVTAFEA", "down_seq": "RTINAIWFLNLAVADFLSCL", "snv": [ { "evidence": [ { "id": "rs2059303114", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2059303114" }, { "id": "rs2059303114", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2059303114" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KRT->NRT).", "chr_id": "19", "chr_pos": "47319978", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K67", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P21730-1.79.79", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P21730-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763699139", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763699139", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763699139", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763699139", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763699139", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763699139#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763699139", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763699139", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VWVTAFEAKRTINAIWFLNL", "down_seq": "VADFLSCLALPILFTSIVQH", "snv": [ { "evidence": [ { "id": "rs763699139", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763699139" }, { "id": "rs763699139", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763699139" }, { "id": "rs763699139", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763699139#frequency_tab" }, { "id": "rs763699139", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763699139" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLT).", "chr_id": "19", "chr_pos": "47320012", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A79", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P21730-1.67.67", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P21730-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of the major phosphorylation sites in human C5a anaphylatoxin receptor in vivo.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Giannini E, Brouchon L, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CINPIIYVVAGQGFQGRLRK", "down_seq": "LPSLLRNVLTEESVVRESKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "site_lbl": "Ser314" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P21730-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P21730-1.334.334", "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": "P21730-1.317.317", "start_pos": 317, "end_pos": 317, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human complement 5a (C5a) anaphylatoxin receptor (CD88) phosphorylation sites and their specific role in receptor phosphorylation and attenuation of G protein-mediated responses. Desensitization of C5a receptor controls superoxide production but not receptor sequestration in HL-60 cells.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Christophe T, Rabiet MJ, Tardif M, Milcent MD, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" } ] }, { "title": "Identification of the major phosphorylation sites in human C5a anaphylatoxin receptor in vivo.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Giannini E, Brouchon L, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PIIYVVAGQGFQGRLRKSLP", "down_seq": "LLRNVLTEESVVRESKSFTR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" }, { "database": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "site_lbl": "Ser317" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P21730-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.314.314", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P21730-1.334.334", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P21730-1.336.336", "categories": [ "mutagenesis_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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P21730-1.327.327", "start_pos": 327, "end_pos": 327, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of the major phosphorylation sites in human C5a anaphylatoxin receptor in vivo.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Giannini E, Brouchon L, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" } ] }, { "title": "Human complement 5a (C5a) anaphylatoxin receptor (CD88) phosphorylation sites and their specific role in receptor phosphorylation and attenuation of G protein-mediated responses. Desensitization of C5a receptor controls superoxide production but not receptor sequestration in HL-60 cells.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Christophe T, Rabiet MJ, Tardif M, Milcent MD, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" } ] }, { "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": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] }, { "title": "Phosphorylation of key serine residues is required for internalization of the complement 5a (C5a) anaphylatoxin receptor via a beta-arrestin, dynamin, and clathrin-dependent pathway.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Braun L, Christophe T, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FQGRLRKSLPSLLRNVLTEE", "down_seq": "VVRESKSFTRSTVDTMAQKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" }, { "database": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" }, { "database": "PubMed", "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600" } ], "site_lbl": "Ser327" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P21730-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P21730-1.314.314", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P21730-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P21730-1.334.334", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P21730-1.336.336", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P21730-1.338.338", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P21730-1.339.339", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P21730-1.342.342", "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": "P21730-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Dynamics of protein kinase C-mediated phosphorylation of the complement C5a receptor on serine 334.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Pollok-Kopp B, Huttenrauch F, Rethorn S, Oppermann M", "evidence": [ { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "17145764", "url": "https://glygen.org/publication/PubMed/17145764" } ] }, { "title": "Human complement 5a (C5a) anaphylatoxin receptor (CD88) phosphorylation sites and their specific role in receptor phosphorylation and attenuation of G protein-mediated responses. Desensitization of C5a receptor controls superoxide production but not receptor sequestration in HL-60 cells.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Christophe T, Rabiet MJ, Tardif M, Milcent MD, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" } ] }, { "title": "Phosphorylation of key serine residues is required for internalization of the complement 5a (C5a) anaphylatoxin receptor via a beta-arrestin, dynamin, and clathrin-dependent pathway.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Braun L, Christophe T, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600" } ] }, { "title": "Identification of the major phosphorylation sites in human C5a anaphylatoxin receptor in vivo.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Giannini E, Brouchon L, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" } ] } ], "crossref": [ { "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17145764", "url": "https://glygen.org/publication/PubMed/17145764", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLPSLLRNVLTEESVVRESK", "down_seq": "FTRSTVDTMAQKTQAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P05771-1", "kinase_gene_name": "PRKCB", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" }, { "database": "PubMed", "id": "17145764", "url": "https://glygen.org/publication/PubMed/17145764" } ], "site_lbl": "Ser334" }, { "kinase_uniprot_canonical_ac": "Q05655-1", "kinase_gene_name": "PRKCD", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" }, { "database": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" }, { "database": "PubMed", "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600" }, { "database": "PubMed", "id": "17145764", "url": "https://glygen.org/publication/PubMed/17145764" } ], "site_lbl": "Ser334" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" }, { "database": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" }, { "database": "PubMed", "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600" }, { "database": "PubMed", "id": "17145764", "url": "https://glygen.org/publication/PubMed/17145764" } ], "site_lbl": "Ser334" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P21730-1.314.314", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P21730-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P21730-1.336.336", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.338.338", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P21730-1.339.339", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P21730-1.342.342", "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": 3 } ], "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": "P21730-1.338.338", "start_pos": 338, "end_pos": 338, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human complement 5a (C5a) anaphylatoxin receptor (CD88) phosphorylation sites and their specific role in receptor phosphorylation and attenuation of G protein-mediated responses. Desensitization of C5a receptor controls superoxide production but not receptor sequestration in HL-60 cells.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Christophe T, Rabiet MJ, Tardif M, Milcent MD, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" } ] }, { "title": "Identification of the major phosphorylation sites in human C5a anaphylatoxin receptor in vivo.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Giannini E, Brouchon L, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" } ] }, { "title": "Phosphorylation of key serine residues is required for internalization of the complement 5a (C5a) anaphylatoxin receptor via a beta-arrestin, dynamin, and clathrin-dependent pathway.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Braun L, Christophe T, Boulay F", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" } ], "reference": [ { "type": "PubMed", "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLRNVLTEESVVRESKSFTR", "down_seq": "TVDTMAQKTQAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "10636859", "url": "https://glygen.org/publication/PubMed/10636859" }, { "database": "PubMed", "id": "7642584", "url": "https://glygen.org/publication/PubMed/7642584" }, { "database": "iPTMnet", "id": "P21730", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P21730" }, { "database": "PubMed", "id": "12464600", "url": "https://glygen.org/publication/PubMed/12464600" } ], "site_lbl": "Ser338" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.334.334", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P21730-1.336.336", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P21730-1.339.339", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P21730-1.342.342", "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": "P21730-1.339.339", "start_pos": 339, "end_pos": 339, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural snapshots uncover a key phosphorylation motif in GPCRs driving \u03b2-arrestin activation.", "journal": "Molecular cell", "date": "2023-06-15", "authors": "Maharana Jagannath, Sarma Parishmita, Yadav Manish K, Saha Sayantan, Singh Vinay, Saha Shirsha, Chami Mohamed, Banerjee Ramanuj, Shukla Arun K", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LRNVLTEESVVRESKSFTRS", "down_seq": "VDTMAQKTQAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686" } ], "site_lbl": "Thr339" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P21730-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P21730-1.334.334", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.336.336", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P21730-1.338.338", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P21730-1.342.342", "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": "P21730-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "P21730-1", "length": 350, "uniprot_id": "C5AR1_HUMAN", "protein_name": "C5a anaphylatoxin chemotactic receptor 1", "refseq_ac": "NP_001727", "refseq_name": "C5a anaphylatoxin chemotactic receptor 1", "gene_name": "C5AR1", "gene_names_uniprotkb": "C5AR1; C5AR; C5R1", "gene_names_refseq": "C5AR1; C5AR; C5A; C5R1; CD88", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural snapshots uncover a key phosphorylation motif in GPCRs driving \u03b2-arrestin activation.", "journal": "Molecular cell", "date": "2023-06-15", "authors": "Maharana Jagannath, Sarma Parishmita, Yadav Manish K, Saha Sayantan, Singh Vinay, Saha Shirsha, Chami Mohamed, Banerjee Ramanuj, Shukla Arun K", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" } ], "reference": [ { "type": "PubMed", "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686" } ] } ], "crossref": [ { "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VLTEESVVRESKSFTRSTVD", "down_seq": "MAQKTQAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P21730", "url": "https://www.uniprot.org/uniprotkb/P21730" }, { "database": "PubMed", "id": "37209686", "url": "https://glygen.org/publication/PubMed/37209686" } ], "site_lbl": "Thr342" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "5", "end_pos": "5" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "22" }, { "start_pos": "2", "end_pos": "30" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "314", "end_pos": "314" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "342", "end_pos": "342" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P21730-1.327.327", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P21730-1.332.332", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P21730-1.334.334", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P21730-1.336.336", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P21730-1.338.338", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P21730-1.339.339", "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": "P22003-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003", "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": "rs751893982", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751893982", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751893982", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751893982", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751893982", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751893982", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EAVTAAEFRIYKDRSNNRFE", "down_seq": "ETIKISIYQIIKEYTNRDAD", "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": "Asn211", "evidence": [ { "id": "P22003", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P22003#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" } ] } ], "snv": [ { "evidence": [ { "id": "rs751893982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751893982" }, { "id": "rs751893982", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751893982" }, { "id": "rs751893982", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751893982" } ], "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": "6", "chr_pos": "55819705", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N211", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P22003-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P22003-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P22003-1.213.213", "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": 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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P22003-1.327.327", "start_pos": 327, "end_pos": 327, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs757915843", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757915843", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757915843", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757915843", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757915843", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757915843#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757915843", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757915843", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ASEVLLRSVRAANKRKNQNR", "down_seq": "KSSSHQDSSRMSSVGDYNTS", "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": "Asn327", "evidence": [ { "id": "P22003", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P22003#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs757915843", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757915843" }, { "id": "rs757915843", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757915843" }, { "id": "rs757915843", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757915843#frequency_tab" }, { "id": "rs757915843", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757915843" } ], "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 (NKS->SKS); n-glyco-sequon-gain (NRN->NRS).", "chr_id": "6", "chr_pos": "55774096", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N327", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P22003-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P22003-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P22003-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P22003-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P22003-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P22003-1.345.345", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P22003-1.347.347", "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": "P22003-1.345.345", "start_pos": 345, "end_pos": 345, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs370514583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370514583", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370514583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370514583", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370514583", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370514583#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs370514583", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370514583", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NRNKSSSHQDSSRMSSVGDY", "down_seq": "TSEQKQACKKHELYVSFRDL", "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": "Asn345", "evidence": [ { "id": "P22003", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P22003#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs370514583", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370514583" }, { "id": "rs370514583", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370514583" }, { "id": "rs370514583", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370514583#frequency_tab" }, { "id": "rs370514583", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370514583" } ], "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": "6", "chr_pos": "55760527", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N345", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P22003-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P22003-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P22003-1.327.327", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P22003-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P22003-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P22003-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P22003-1.359.359", "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": "P22003-1.395.395", "start_pos": 395, "end_pos": 395, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1198782595", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1198782595", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1198782595", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1198782595", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EGYAAFYCDGECSFPLNAHM", "down_seq": "ATNHAIVQTLVHLMFPDHVP", "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": "Asn395", "evidence": [ { "id": "P22003", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P22003#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" }, { "id": "rs1198782595", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1198782595" }, { "id": "rs1198782595", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1198782595" } ], "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 (NAT->SAT).", "chr_id": "6", "chr_pos": "55759036", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N395", "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", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P22003-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P22003-1.400.400", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MVAFFKASEVLLRSVRAANK", "down_seq": "KNQNRNKSSSHQDSSRMSSV", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "22", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 3 filters: patient freq. (1.1%); patient count (22/2053); num. of cancers (7).", "chr_id": "6", "chr_pos": "55774114", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R321", "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: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: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: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": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "6", "chr_pos": "55774115", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R321", "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: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" } ] }, { "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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P22003-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P22003-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P22003-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P22003-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P22003-1.327.327", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P22003-1.334.334", "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": 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": "P22003-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GDNHVHSSFIYRRLRNHERR", "down_seq": "IQREILSILGLPHRPRPFSP", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "13", "frequency": "0.6", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 2 filters: patient count (13/2053); num. of cancers (3).", "chr_id": "6", "chr_pos": "55874718", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E50", "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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P22003-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P22003-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P22003-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P22003-1.47.47", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773656870", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773656870", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773656870", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773656870", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773656870", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773656870#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773656870", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773656870", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ASLAEETRGARKGYPASPNG", "down_seq": "PRRIQLSRTTPLTTQSPPLA", "snv": [ { "evidence": [ { "id": "rs773656870", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773656870" }, { "id": "rs773656870", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773656870" }, { "id": "rs773656870", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773656870#frequency_tab" }, { "id": "rs773656870", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773656870" } ], "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": "6", "chr_pos": "55874498", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y123", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P22003-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P22003-1.132.132", "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": "P22003-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AEETRGARKGYPASPNGYPR", "down_seq": "IQLSRTTPLTTQSPPLASLH", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "55874489", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R126", "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: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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P22003-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P22003-1.132.132", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ARKGYPASPNGYPRRIQLSR", "down_seq": "TPLTTQSPPLASLHDTNFLN", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "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 (4).", "chr_id": "6", "chr_pos": "55874471", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T132", "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: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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P22003-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P22003-1.126.126", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NFLNDADMVMSFVNLVERDK", "down_seq": "FSHQRRHYKEFRFDLTQIPH", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "6", "frequency": "0.3", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DFS->NFS).", "chr_id": "6", "chr_pos": "55819833", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D169", "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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P22003-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P22003-1.183.183", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VNLVERDKDFSHQRRHYKEF", "down_seq": "FDLTQIPHGEAVTAAEFRIY", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "55819797", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R181", "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": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P22003-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P22003-1.183.183", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1239156046", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1239156046", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1239156046", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1239156046", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LVERDKDFSHQRRHYKEFRF", "down_seq": "LTQIPHGEAVTAAEFRIYKD", "snv": [ { "evidence": [ { "id": "rs1239156046", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1239156046" }, { "id": "rs1239156046", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1239156046" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLT->NLT).", "chr_id": "6", "chr_pos": "55819791", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D183", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P22003-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P22003-1.181.181", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PHGEAVTAAEFRIYKDRSNN", "down_seq": "FENETIKISIYQIIKEYTNR", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "55819715", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R208", "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: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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P22003-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P22003-1.211.211", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P22003-1.213.213", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2127538500", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127538500", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2127538500", "url": "https://www.ensembl.org/id/rs2127538500", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "HGEAVTAAEFRIYKDRSNNR", "down_seq": "ENETIKISIYQIIKEYTNRD", "snv": [ { "evidence": [ { "id": "rs2127538500", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127538500" }, { "id": "rs2127538500", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127538500" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRF->NRS).", "chr_id": "6", "chr_pos": "55819712", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F209", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P22003-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P22003-1.211.211", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P22003-1.213.213", "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": "P22003-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VTAAEFRIYKDRSNNRFENE", "down_seq": "IKISIYQIIKEYTNRDADLF", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NET->NEI).", "chr_id": "6", "chr_pos": "55819700", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T213", "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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P22003-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P22003-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P22003-1.211.211", "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": "P22003-1.279.279", "start_pos": 279, "end_pos": 279, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WVINPQNNLGLQLCAETGDG", "down_seq": "SINVKSAGLVGRQGPQSKQP", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "55774241", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R279", "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: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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "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": "P22003-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs9475437", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9475437", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs9475437", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs9475437", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs9475437", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9475437", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs9475437", "url": "https://www.ncbi.nlm.nih.gov/snp/rs9475437#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs9475437", "url": "http://gnomad.broadinstitute.org/awesome?query=rs9475437", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "M", "down_seq": "LTVFLLKGIVGFLWSCWVLV", "snv": [ { "evidence": [ { "id": "rs9475437", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9475437" }, { "id": "rs9475437", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs9475437" }, { "id": "rs9475437", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9475437" }, { "id": "rs9475437", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs9475437#frequency_tab" }, { "id": "rs9475437", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs9475437" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HLT->NLT).", "chr_id": "6", "chr_pos": "55874862", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H2", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P22003-1.4.4", "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": "P22003-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1012924212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1012924212", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1012924212", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1012924212#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1012924212", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1012924212", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AGLVGRQGPQSKQPFMVAFF", "down_seq": "ASEVLLRSVRAANKRKNQNR", "snv": [ { "evidence": [ { "id": "rs1012924212", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1012924212" }, { "id": "rs1012924212", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1012924212#frequency_tab" }, { "id": "rs1012924212", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1012924212" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAS->NAS).", "chr_id": "6", "chr_pos": "55774158", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K306", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P22003-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P22003-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P22003-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P22003-1.326.326", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GPQSKQPFMVAFFKASEVLL", "down_seq": "SVRAANKRKNQNRNKSSSHQ", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "9", "frequency": "0.4", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "55774139", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R313", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P22003-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P22003-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P22003-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P22003-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P22003-1.327.327", "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": "P22003-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1562031131", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1562031131", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1562031131", "url": "https://www.ensembl.org/id/rs1562031131", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FKASEVLLRSVRAANKRKNQ", "down_seq": "RNKSSSHQDSSRMSSVGDYN", "snv": [ { "evidence": [ { "id": "rs1562031131", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1562031131" }, { "id": "rs1562031131", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1562031131" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQN->NQT).", "chr_id": "6", "chr_pos": "55774102", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N325", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P22003-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P22003-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P22003-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P22003-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P22003-1.327.327", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P22003-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P22003-1.345.345", "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": "P22003-1.326.326", "start_pos": 326, "end_pos": 326, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KASEVLLRSVRAANKRKNQN", "down_seq": "NKSSSHQDSSRMSSVGDYNT", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "6", "chr_pos": "55774099", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R326", "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: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: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: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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P22003-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P22003-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P22003-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P22003-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P22003-1.327.327", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P22003-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P22003-1.345.345", "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": "P22003-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SVRAANKRKNQNRNKSSSHQ", "down_seq": "SSRMSSVGDYNTSEQKQACK", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "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 (DSS->NSS).", "chr_id": "6", "chr_pos": "55774076", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D334", "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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P22003-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P22003-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P22003-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P22003-1.327.327", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P22003-1.345.345", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P22003-1.347.347", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.347.347", "start_pos": 347, "end_pos": 347, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776849073", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776849073", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776849073", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776849073", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776849073", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776849073", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2481611244", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2481611244", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NKSSSHQDSSRMSSVGDYNT", "down_seq": "EQKQACKKHELYVSFRDLGW", "snv": [ { "evidence": [ { "id": "rs776849073", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776849073" }, { "id": "rs776849073", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776849073" }, { "id": "rs776849073", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776849073" } ], "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": "6", "chr_pos": "55760521", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S347", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2481611244", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2481611244" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->NTR).", "chr_id": "6", "chr_pos": "55760520", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S347", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P22003-1.327.327", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P22003-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P22003-1.345.345", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P22003-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P22003-1.359.359", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P22003-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RMSSVGDYNTSEQKQACKKH", "down_seq": "LYVSFRDLGWQDWIIAPEGY", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "9", "frequency": "0.4", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "55760492", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E357", "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": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P22003-1.345.345", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P22003-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P22003-1.359.359", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.359.359", "start_pos": 359, "end_pos": 359, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SSVGDYNTSEQKQACKKHEL", "down_seq": "VSFRDLGWQDWIIAPEGYAA", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (YVS->NVS).", "chr_id": "6", "chr_pos": "55760486", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y359", "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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P22003-1.345.345", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P22003-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P22003-1.357.357", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1259795109", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1259795109", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1259795109", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1259795109", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LWSCWVLVGYAKGGLGDNHV", "down_seq": "SSFIYRRLRNHERREIQREI", "snv": [ { "evidence": [ { "id": "rs1259795109", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1259795109" }, { "id": "rs1259795109", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1259795109" } ], "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": "6", "chr_pos": "55874763", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H35", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P22003-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P22003-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P22003-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P22003-1.50.50", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YAAFYCDGECSFPLNAHMNA", "down_seq": "NHAIVQTLVHLMFPDHVPKP", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NAT->NAN).", "chr_id": "6", "chr_pos": "55759030", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T397", "disease": [ { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P22003-1.395.395", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P22003-1.400.400", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1351901968", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1351901968", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1351901968", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1351901968", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FYCDGECSFPLNAHMNATNH", "down_seq": "IVQTLVHLMFPDHVPKPCCA", "snv": [ { "evidence": [ { "id": "rs1351901968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1351901968" }, { "id": "rs1351901968", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1351901968" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHA->NHS).", "chr_id": "6", "chr_pos": "55759022", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A400", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" }, { "id": "rs1351901968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1351901968" }, { "id": "rs1351901968", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1351901968" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NHA->NHT).", "chr_id": "6", "chr_pos": "55759022", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A400", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P22003-1.395.395", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P22003-1.397.397", "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": 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": "P22003-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LVGYAKGGLGDNHVHSSFIY", "down_seq": "RLRNHERREIQREILSILGL", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "1704", "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": "55874744", "ref_nt": "C", "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: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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P22003-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P22003-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P22003-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P22003-1.50.50", "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": "P22003-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VGYAKGGLGDNHVHSSFIYR", "down_seq": "LRNHERREIQREILSILGLP", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "55874741", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R42", "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: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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P22003-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P22003-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P22003-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P22003-1.50.50", "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": "P22003-1.439.439", "start_pos": 439, "end_pos": 439, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "CAPTKLNAISVLYFDDSSNV", "down_seq": "LKKYRNMVVRSCGCH", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "I", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVI->NVS).", "chr_id": "6", "chr_pos": "55755582", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "I439", "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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P22003-1.449.449", "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": "P22003-1.449.449", "start_pos": 449, "end_pos": 449, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VLYFDDSSNVILKKYRNMVV", "down_seq": "SCGCH", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "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 (5).", "chr_id": "6", "chr_pos": "55755553", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R449", "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: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: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: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": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P22003-1.439.439", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22003-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22003", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GGLGDNHVHSSFIYRRLRNH", "down_seq": "RREIQREILSILGLPHRPRP", "snv": [ { "evidence": [ { "id": "P22003", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22003" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "6", "chr_pos": "55874727", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E47", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P22003-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P22003-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P22003-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P22003-1.50.50", "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": "P22003-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P22003-1", "length": 454, "uniprot_id": "BMP5_HUMAN", "protein_name": "Bone morphogenetic protein 5", "refseq_ac": "NP_001316683", "refseq_name": "bone morphogenetic protein 5 isoform 2 precursor", "gene_name": "BMP5", "gene_names_uniprotkb": "BMP5", "gene_names_refseq": "BMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22003", "url": "https://www.uniprot.org/uniprotkb/P22003" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P22003-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P22003-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "P22003", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P22003", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MHL", "down_seq": "VFLLKGIVGFLWSCWVLVGY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P22003", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P22003" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Thr4" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "395", "end_pos": "395" } ] }, { "type": "snv", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P22003-1.2.2", "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": "P22362-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "P22362-1", "length": 96, "uniprot_id": "CCL1_HUMAN", "protein_name": "C-C motif chemokine 1", "refseq_ac": "NP_002972", "refseq_name": "C-C motif chemokine 1 precursor", "gene_name": "CCL1", "gene_names_uniprotkb": "CCL1; SCYA1", "gene_names_refseq": "CCL1; I-309; P500; SCYA1; SISe; TCA3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22362", "url": "https://www.uniprot.org/uniprotkb/P22362" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22362", "url": "https://www.uniprot.org/uniprotkb/P22362", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "4OIK", "url": "https://www.rcsb.org/structure/4OIK", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8U1U", "url": "https://www.rcsb.org/structure/8U1U", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4OIK|B|30", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "4OIK|A|30", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8U1U|A|52", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RCCFSFAEQEIPLRAILCYR", "down_seq": "TSSICSNEGLIFKLKRGKEA", "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": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=4OIK&bu=0&command=select+.B:30;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn52", "evidence": [ { "id": "P22362", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P22362#ptm_processing" }, { "id": "4OIK", "database": "PDB", "url": "https://www.rcsb.org/structure/4OIK" }, { "id": "8U1U", "database": "PDB", "url": "https://www.rcsb.org/structure/8U1U" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "52", "end_pos": "52" } ] }, { "type": "snv", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "74", "end_pos": "74" } ] } ], "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": 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", "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": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P22362-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "P22362-1", "length": 96, "uniprot_id": "CCL1_HUMAN", "protein_name": "C-C motif chemokine 1", "refseq_ac": "NP_002972", "refseq_name": "C-C motif chemokine 1 precursor", "gene_name": "CCL1", "gene_names_uniprotkb": "CCL1; SCYA1", "gene_names_refseq": "CCL1; I-309; P500; SCYA1; SISe; TCA3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22362", "url": "https://www.uniprot.org/uniprotkb/P22362" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22362", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22362", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IITTALVCLLLAGMWPEDVD", "down_seq": "KSMQVPFSRCCFSFAEQEIP", "snv": [ { "evidence": [ { "id": "P22362", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22362" } ], "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 (SKS->NKS).", "chr_id": "17", "chr_pos": "34363094", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S23", "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": "52", "end_pos": "52" } ] }, { "type": "snv", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "74", "end_pos": "74" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P22362-1.4.4", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22362-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P22362-1", "length": 96, "uniprot_id": "CCL1_HUMAN", "protein_name": "C-C motif chemokine 1", "refseq_ac": "NP_002972", "refseq_name": "C-C motif chemokine 1 precursor", "gene_name": "CCL1", "gene_names_uniprotkb": "CCL1; SCYA1", "gene_names_refseq": "CCL1; I-309; P500; SCYA1; SISe; TCA3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22362", "url": "https://www.uniprot.org/uniprotkb/P22362" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22362", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22362", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "MQI", "down_seq": "TTALVCLLLAGMWPEDVDSK", "snv": [ { "evidence": [ { "id": "P22362", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22362" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (ITT->NTT).", "chr_id": "17", "chr_pos": "34363151", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "I4", "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": "52", "end_pos": "52" } ] }, { "type": "snv", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "74", "end_pos": "74" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P22362-1.23.23", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P22362-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "P22362-1", "length": 96, "uniprot_id": "CCL1_HUMAN", "protein_name": "C-C motif chemokine 1", "refseq_ac": "NP_002972", "refseq_name": "C-C motif chemokine 1 precursor", "gene_name": "CCL1", "gene_names_uniprotkb": "CCL1; SCYA1", "gene_names_refseq": "CCL1; I-309; P500; SCYA1; SISe; TCA3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22362", "url": "https://www.uniprot.org/uniprotkb/P22362" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P22362", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22362", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SSICSNEGLIFKLKRGKEAC", "down_seq": "LDTVGWVQRHRKMLRHCPSK", "snv": [ { "evidence": [ { "id": "P22362", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22362" } ], "glycoeffect": [], "subjects_tested": "4799", "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": "34360630", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A74", "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: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: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": "52", "end_pos": "52" } ] }, { "type": "snv", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "74", "end_pos": "74" } ] } ], "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": "P31358-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "P31358-1", "length": 61, "uniprot_id": "CD52_HUMAN", "protein_name": "CAMPATH-1 antigen", "refseq_ac": "NP_001794", "refseq_name": "CAMPATH-1 antigen precursor", "gene_name": "CD52", "gene_names_uniprotkb": "CD52; CDW52; HE5", "gene_names_refseq": "CD52; CDW52; EDDM5; HE5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Specific Sialoforms Required for the Immune Suppressive Activity of Human Soluble CD52.", "journal": "Frontiers in immunology", "date": "2019", "authors": "Shathili Abdulrahman M, Bandala-Sanchez Esther, John Alan, Goddard-Borger Ethan D, Thaysen-Andersen Morten, Everest-Dass Arun V, Adams Timothy E, Harrison Leonard C, Packer Nicolle H", "evidence": [ { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "31507595", "url": "https://glygen.org/publication/PubMed/31507595" } ] } ], "crossref": [ { "id": "31507595", "url": "https://glygen.org/publication/PubMed/31507595", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1308985261", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1308985261", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1308985261", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1308985261", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MKRFLFLLLTI", "down_seq": "LLVMVQIQTGLSGQNDTSQT", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "automatic_literature_mining", "site_category_dict": { "automatic_literature_mining": true }, "site_seq": "S", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser12", "evidence": [ { "id": "31507595", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31507595" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] } ], "snv": [ { "evidence": [ { "id": "rs1308985261", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1308985261" }, { "id": "rs1308985261", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1308985261" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->N).", "chr_id": "1", "chr_pos": "26318052", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S12", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P31358-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P31358-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P31358-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P31358-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P31358-1.29.29", "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", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "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", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P31358-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P31358-1", "length": 61, "uniprot_id": "CD52_HUMAN", "protein_name": "CAMPATH-1 antigen", "refseq_ac": "NP_001794", "refseq_name": "CAMPATH-1 antigen precursor", "gene_name": "CD52", "gene_names_uniprotkb": "CD52; CDW52; HE5", "gene_names_refseq": "CD52; CDW52; EDDM5; HE5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P31358", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs763079859", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763079859", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763079859", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763079859", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763079859", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763079859", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LLLTISLLVMVQIQTGLSGQ", "down_seq": "DTSQTSSPSASSNISGGIFL", "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": "Asn27", "evidence": [ { "id": "P31358", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P31358#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "P31358", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NDT->HDT).", "chr_id": "1", "chr_pos": "26320195", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N27", "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": "rs763079859", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763079859" }, { "id": "rs763079859", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763079859" }, { "id": "rs763079859", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763079859" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDT->TDT).", "chr_id": "1", "chr_pos": "26320196", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N27", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P31358-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P31358-1.12.12", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P31358-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P31358-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P31358-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P31358-1.42.42", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "P31358-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "P31358-1", "length": 61, "uniprot_id": "CD52_HUMAN", "protein_name": "CAMPATH-1 antigen", "refseq_ac": "NP_001794", "refseq_name": "CAMPATH-1 antigen precursor", "gene_name": "CD52", "gene_names_uniprotkb": "CD52; CDW52; HE5", "gene_names_refseq": "CD52; CDW52; EDDM5; HE5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P31358", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1071849", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1071849", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1071849", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1071849", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs1071849", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1071849", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs1071849", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1071849#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1071849", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1071849", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QTGLSGQNDTSQTSSPSASS", "down_seq": "ISGGIFLFFVANAIIHLFCF", "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": "Asn40", "evidence": [ { "id": "P31358", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P31358#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "P31358", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358" }, { "id": "rs1071849", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1071849" }, { "id": "rs1071849", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1071849" }, { "id": "rs1071849", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1071849" }, { "id": "rs1071849", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1071849#frequency_tab" }, { "id": "rs1071849", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1071849" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "9251", "subjects_positive": "3", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NIS->SIS).", "chr_id": "1", "chr_pos": "26320235", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N40", "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", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P31358-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P31358-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P31358-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P31358-1.42.42", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P31358-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P31358-1", "length": 61, "uniprot_id": "CD52_HUMAN", "protein_name": "CAMPATH-1 antigen", "refseq_ac": "NP_001794", "refseq_name": "CAMPATH-1 antigen precursor", "gene_name": "CD52", "gene_names_uniprotkb": "CD52; CDW52; HE5", "gene_names_refseq": "CD52; CDW52; EDDM5; HE5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs77928789", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs77928789", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs77928789", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs77928789", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs77928789", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs77928789", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs77928789", "url": "https://www.ncbi.nlm.nih.gov/snp/rs77928789#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs77928789", "url": "http://gnomad.broadinstitute.org/awesome?query=rs77928789", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MKRFLFLLL", "down_seq": "ISLLVMVQIQTGLSGQNDTS", "snv": [ { "evidence": [ { "id": "rs77928789", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs77928789" }, { "id": "rs77928789", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs77928789" }, { "id": "rs77928789", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs77928789" }, { "id": "rs77928789", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs77928789#frequency_tab" }, { "id": "rs77928789", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs77928789" } ], "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 (TIS->NIS).", "chr_id": "1", "chr_pos": "26318046", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T10", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P31358-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P31358-1.12.12", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P31358-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P31358-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P31358-1.29.29", "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": "P31358-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P31358-1", "length": 61, "uniprot_id": "CD52_HUMAN", "protein_name": "CAMPATH-1 antigen", "refseq_ac": "NP_001794", "refseq_name": "CAMPATH-1 antigen precursor", "gene_name": "CD52", "gene_names_uniprotkb": "CD52; CDW52; HE5", "gene_names_refseq": "CD52; CDW52; EDDM5; HE5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P31358", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2073839855", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2073839855", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2073839855", "url": "https://www.ensembl.org/id/rs2073839855", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLTISLLVMVQIQTGLSGQN", "down_seq": "TSQTSSPSASSNISGGIFLF", "snv": [ { "evidence": [ { "id": "P31358", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358" }, { "id": "rs2073839855", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2073839855" }, { "id": "rs2073839855", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2073839855" } ], "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 (DTS->NTS).", "chr_id": "1", "chr_pos": "26320198", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D28", "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": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P31358-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P31358-1.12.12", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P31358-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P31358-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P31358-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P31358-1.42.42", "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": "P31358-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P31358-1", "length": 61, "uniprot_id": "CD52_HUMAN", "protein_name": "CAMPATH-1 antigen", "refseq_ac": "NP_001794", "refseq_name": "CAMPATH-1 antigen precursor", "gene_name": "CD52", "gene_names_uniprotkb": "CD52; CDW52; HE5", "gene_names_refseq": "CD52; CDW52; EDDM5; HE5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2073839945", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2073839945", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2073839945", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2073839945#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774596319", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774596319", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774596319", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774596319", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774596319", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774596319", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LTISLLVMVQIQTGLSGQND", "down_seq": "SQTSSPSASSNISGGIFLFF", "snv": [ { "evidence": [ { "id": "rs2073839945", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2073839945" }, { "id": "rs2073839945", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2073839945#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 (NDT->NDI).", "chr_id": "1", "chr_pos": "26320202", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T29", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774596319", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774596319" }, { "id": "rs774596319", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774596319" }, { "id": "rs774596319", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774596319" } ], "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 (NDT->NDP).", "chr_id": "1", "chr_pos": "26320201", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T29", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P31358-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P31358-1.12.12", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P31358-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P31358-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P31358-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P31358-1.42.42", "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": 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": "P31358-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P31358-1", "length": 61, "uniprot_id": "CD52_HUMAN", "protein_name": "CAMPATH-1 antigen", "refseq_ac": "NP_001794", "refseq_name": "CAMPATH-1 antigen precursor", "gene_name": "CD52", "gene_names_uniprotkb": "CD52; CDW52; HE5", "gene_names_refseq": "CD52; CDW52; EDDM5; HE5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P31358", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MK", "down_seq": "FLFLLLTISLLVMVQIQTGL", "snv": [ { "evidence": [ { "id": "P31358", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358" } ], "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": "26318024", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R3", "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: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" ] }, { "evidence": [ { "id": "P31358", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P31358" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "26318025", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R3", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P31358-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P31358-1.12.12", "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": 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": "P31358-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P31358-1", "length": 61, "uniprot_id": "CD52_HUMAN", "protein_name": "CAMPATH-1 antigen", "refseq_ac": "NP_001794", "refseq_name": "CAMPATH-1 antigen precursor", "gene_name": "CD52", "gene_names_uniprotkb": "CD52; CDW52; HE5", "gene_names_refseq": "CD52; CDW52; EDDM5; HE5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P31358", "url": "https://www.uniprot.org/uniprotkb/P31358" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1256347714", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1256347714", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1256347714", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1256347714", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750360671", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750360671", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750360671", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750360671", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750360671", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750360671#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750360671", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750360671", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GLSGQNDTSQTSSPSASSNI", "down_seq": "GGIFLFFVANAIIHLFCFS", "snv": [ { "evidence": [ { "id": "rs1256347714", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1256347714" }, { "id": "rs1256347714", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1256347714" } ], "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 (NIS->NIN).", "chr_id": "1", "chr_pos": "26320241", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S42", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750360671", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750360671" }, { "id": "rs750360671", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750360671" }, { "id": "rs750360671", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750360671#frequency_tab" }, { "id": "rs750360671", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750360671" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIS->NIR).", "chr_id": "1", "chr_pos": "26320242", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S42", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P31358-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P31358-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P31358-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P31358-1.40.40", "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": "P40259-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cryo-EM structure of the human IgM B cell receptor.", "journal": "Science (New York, N.Y.)", "date": "2022-08-19", "authors": "Su Qiang, Chen Mengying, Shi Yan, Zhang Xiaofeng, Huang Gaoxingyu, Huang Bangdong, Liu Dongwei, Liu Zhangsuo, Shi Yigong", "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259#ptm_processing" }, { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "reference": [ { "type": "PubMed", "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043" } ] }, { "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": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7XQ8", "url": "https://www.rcsb.org/structure/7XQ8", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043", "database": "PubMed", "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": "7XT6", "url": "https://www.rcsb.org/structure/7XT6", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7XQ8|B|101", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7XT6|C|101", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EMDENPQQLKLEKGRMEESQ", "down_seq": "ESLATLTIQGIRFEDNGIYF", "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": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7XQ8&bu=0&command=select+.B:101;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "P40259", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40259#ptm_processing" }, { "id": "7XQ8", "database": "PDB", "url": "https://www.rcsb.org/sequence/7XQ8" }, { "id": "35981043", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35981043" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "7XT6", "database": "PDB", "url": "https://www.rcsb.org/structure/7XT6" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40259-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40259-1.106.106", "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", "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": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P40259-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259", "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": "rs370893971", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370893971", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370893971", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370893971", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370893971", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370893971", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1908029394", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1908029394", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1908029394", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1908029394", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1908029394", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1908029394", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LTIQGIRFEDNGIYFCQQKC", "down_seq": "NTSEVYQGCGTELRVMGFST", "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": "Asn127", "evidence": [ { "id": "P40259", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40259#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" } ] } ], "snv": [ { "evidence": [ { "id": "rs370893971", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370893971" }, { "id": "rs370893971", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370893971" }, { "id": "rs370893971", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370893971" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNT->DNT).", "chr_id": "17", "chr_pos": "63930125", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N127", "disease": [ { "disease_id": "DOID:0081138", "recommended_name": { "id": "DOID:0081138", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0081138", "name": "agammaglobulinemia 6", "description": "An agammaglobulinemia that has_material_basis_in homozygous mutation in the CD79B gene on chromosome 17q23." }, "synonyms": [ { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "Any autosomal agammaglobulinemia in which the cause of the disease is a mutation in the CD79B gene." }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "CD79B autosomal agammaglobulinemia", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "autosomal agammaglobulinemia caused by mutation in CD79B", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "AGM6", "description": "" }, { "id": "MIM:612692", "resource": "MIM", "url": "https://www.omim.org/entry/612692", "name": "Agammaglobulinemia 6, autosomal recessive", "description": "Agammaglobulinemia 6, autosomal recessive" } ], "unlinked_id_list": [], "evidence": [ { "id": "612692", "database": "MIM", "url": "https://www.omim.org/entry/612692" }, { "id": "0081138", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0081138" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1908029394", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1908029394" }, { "id": "rs1908029394", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1908029394" }, { "id": "rs1908029394", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1908029394" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NNT->SNT).", "chr_id": "17", "chr_pos": "63930124", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N127", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40259-1.128.128", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40259-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40259-1.130.130", "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": 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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40259-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259", "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": "rs1024124060", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1024124060", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1024124060", "url": "https://www.ensembl.org/id/rs1024124060", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P40259", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TIQGIRFEDNGIYFCQQKCN", "down_seq": "TSEVYQGCGTELRVMGFSTL", "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": "Asn128", "evidence": [ { "id": "P40259", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40259#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" } ] } ], "snv": [ { "evidence": [ { "id": "rs1024124060", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1024124060" }, { "id": "rs1024124060", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1024124060" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->HTS).", "chr_id": "17", "chr_pos": "63930122", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N128", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P40259", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NTS->KTS).", "chr_id": "17", "chr_pos": "63930123", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N128", "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": "P40259", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NTS->STS).", "chr_id": "17", "chr_pos": "63930124", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N128", "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": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40259-1.127.127", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40259-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40259-1.130.130", "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": 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": 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": "P40259-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QSPRFIARKRGFTVKMHCYM", "down_seq": "SASGNVSWLWKQEMDENPQQ", "glycosylation": [ { "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": "Asn68", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P40259-1.55.57", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40259-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40259-1.73.73", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40259-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cryo-EM structure of the human IgM B cell receptor.", "journal": "Science (New York, N.Y.)", "date": "2022-08-19", "authors": "Su Qiang, Chen Mengying, Shi Yan, Zhang Xiaofeng, Huang Gaoxingyu, Huang Bangdong, Liu Dongwei, Liu Zhangsuo, Shi Yigong", "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259#ptm_processing" }, { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "reference": [ { "type": "PubMed", "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043" } ] }, { "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": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7XQ8", "url": "https://www.rcsb.org/structure/7XQ8", "database": "PDB", "categories": [ "3D Structure" ] }, { "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": "7XT6", "url": "https://www.rcsb.org/structure/7XT6", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7XQ8|B|73", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7XT6|C|73", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs548645671", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548645671", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs548645671", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548645671", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs548645671", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548645671", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs548645671", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548645671#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs548645671", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548645671", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs751709540", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751709540", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751709540", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751709540", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751709540", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751709540#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751709540", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751709540", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200126941", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200126941", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200126941", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200126941", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200126941", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200126941", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200126941", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200126941#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200126941", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200126941", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200126941", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200126941", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IARKRGFTVKMHCYMNSASG", "down_seq": "VSWLWKQEMDENPQQLKLEK", "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": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7XQ8&bu=0&command=select+.B:73;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn73", "evidence": [ { "id": "P40259", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40259#ptm_processing" }, { "id": "35981043", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35981043" }, { "id": "7XQ8", "database": "PDB", "url": "https://www.rcsb.org/sequence/7XQ8" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "7XT6", "database": "PDB", "url": "https://www.rcsb.org/structure/7XT6" } ] } ], "snv": [ { "evidence": [ { "id": "rs548645671", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548645671" }, { "id": "rs548645671", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548645671" }, { "id": "rs548645671", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548645671" }, { "id": "rs548645671", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548645671#frequency_tab" }, { "id": "rs548645671", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548645671" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->DVS).", "chr_id": "17", "chr_pos": "63930287", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N73", "disease": [ { "disease_id": "DOID:0081138", "recommended_name": { "id": "DOID:0081138", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0081138", "name": "agammaglobulinemia 6", "description": "An agammaglobulinemia that has_material_basis_in homozygous mutation in the CD79B gene on chromosome 17q23." }, "synonyms": [ { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "Any autosomal agammaglobulinemia in which the cause of the disease is a mutation in the CD79B gene." }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "CD79B autosomal agammaglobulinemia", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "autosomal agammaglobulinemia caused by mutation in CD79B", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "AGM6", "description": "" }, { "id": "MIM:612692", "resource": "MIM", "url": "https://www.omim.org/entry/612692", "name": "Agammaglobulinemia 6, autosomal recessive", "description": "Agammaglobulinemia 6, autosomal recessive" } ], "unlinked_id_list": [], "evidence": [ { "id": "612692", "database": "MIM", "url": "https://www.omim.org/entry/612692" }, { "id": "0081138", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0081138" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs751709540", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751709540" }, { "id": "rs751709540", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751709540" }, { "id": "rs751709540", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751709540#frequency_tab" }, { "id": "rs751709540", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751709540" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->KVS).", "chr_id": "17", "chr_pos": "63930285", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N73", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200126941", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200126941" }, { "id": "rs200126941", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200126941" }, { "id": "rs200126941", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200126941" }, { "id": "rs200126941", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200126941#frequency_tab" }, { "id": "rs200126941", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200126941" }, { "id": "rs200126941", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200126941" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NVS->TVS).", "chr_id": "17", "chr_pos": "63930286", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N73", "disease": [ { "disease_id": "DOID:0081138", "recommended_name": { "id": "DOID:0081138", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0081138", "name": "agammaglobulinemia 6", "description": "An agammaglobulinemia that has_material_basis_in homozygous mutation in the CD79B gene on chromosome 17q23." }, "synonyms": [ { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "Any autosomal agammaglobulinemia in which the cause of the disease is a mutation in the CD79B gene." }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "CD79B autosomal agammaglobulinemia", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "autosomal agammaglobulinemia caused by mutation in CD79B", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "AGM6", "description": "" }, { "id": "MIM:612692", "resource": "MIM", "url": "https://www.omim.org/entry/612692", "name": "Agammaglobulinemia 6, autosomal recessive", "description": "Agammaglobulinemia 6, autosomal recessive" } ], "unlinked_id_list": [], "evidence": [ { "id": "612692", "database": "MIM", "url": "https://www.omim.org/entry/612692" }, { "id": "0081138", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0081138" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40259-1.55.57", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40259-1.68.68", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40259-1.70.70", "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", "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": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 2 } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40259-1.161.161", "start_pos": 161, "end_pos": 161, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cryo-EM structure of the human IgM B cell receptor.", "journal": "Science (New York, N.Y.)", "date": "2022-08-19", "authors": "Su Qiang, Chen Mengying, Shi Yan, Zhang Xiaofeng, Huang Gaoxingyu, Huang Bangdong, Liu Dongwei, Liu Zhangsuo, Shi Yigong", "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259#ptm_processing" }, { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "reference": [ { "type": "PubMed", "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043" } ] } ], "crossref": [ { "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RVMGFSTLAQLKQRNTLKDG", "down_seq": "IMIQTLLIILFIIVPIFLLL", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "W", "comment": "Blocks IgMBCR assembly.", "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" }, { "database": "PubMed", "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "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": "P40259-1.55.57", "start_pos": 55, "end_pos": 57, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cryo-EM structure of the human IgM B cell receptor.", "journal": "Science (New York, N.Y.)", "date": "2022-08-19", "authors": "Su Qiang, Chen Mengying, Shi Yan, Zhang Xiaofeng, Huang Gaoxingyu, Huang Bangdong, Liu Dongwei, Liu Zhangsuo, Shi Yigong", "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259#ptm_processing" }, { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "reference": [ { "type": "PubMed", "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043" } ] } ], "crossref": [ { "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "RKR", "start_aa": "R", "up_seq": "YRNPKGSACSRIWQSPRFIA", "down_seq": "GFTVKMHCYMNSASGNVSWL", "mutagenesis": [ { "sequence_org": "RKR", "sequence_mut": "AAA", "comment": "Blocks IgMBCR assembly.", "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" }, { "database": "PubMed", "id": "35981043", "url": "https://glygen.org/publication/PubMed/35981043" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P40259-1.68.68", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40259-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40259-1.73.73", "categories": [ "glycosylation_flag", "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": "P40259-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1567810193", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567810193", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1567810193", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1567810193#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1567810193", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1567810193", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1567810193", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1567810193", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PQQLKLEKGRMEESQNESLA", "down_seq": "LTIQGIRFEDNGIYFCQQKC", "snv": [ { "evidence": [ { "id": "rs1567810193", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567810193" }, { "id": "rs1567810193", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1567810193#frequency_tab" }, { "id": "rs1567810193", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1567810193" }, { "id": "rs1567810193", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1567810193" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TLT->NLT).", "chr_id": "17", "chr_pos": "63930187", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T106", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40259-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40259-1.101.101", "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": "P40259-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P40259", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IQGIRFEDNGIYFCQQKCNN", "down_seq": "SEVYQGCGTELRVMGFSTLA", "snv": [ { "evidence": [ { "id": "P40259", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NNT->NNA).", "chr_id": "17", "chr_pos": "63930119", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T129", "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": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40259-1.127.127", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40259-1.128.128", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40259-1.130.130", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40259-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P40259", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1389559363", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1389559363", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1389559363", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1389559363#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1389559363", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1389559363", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1389559363", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1389559363", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QGIRFEDNGIYFCQQKCNNT", "down_seq": "EVYQGCGTELRVMGFSTLAQ", "snv": [ { "evidence": [ { "id": "P40259", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259" }, { "id": "rs1389559363", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1389559363" }, { "id": "rs1389559363", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1389559363#frequency_tab" }, { "id": "rs1389559363", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1389559363" }, { "id": "rs1389559363", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1389559363" } ], "glycoeffect": [ "n-glyco-sequon-loss", "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: n-glyco-sequon-loss (NTS->NTL).", "chr_id": "17", "chr_pos": "63930115", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S130", "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:0081138", "recommended_name": { "id": "DOID:0081138", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0081138", "name": "agammaglobulinemia 6", "description": "An agammaglobulinemia that has_material_basis_in homozygous mutation in the CD79B gene on chromosome 17q23." }, "synonyms": [ { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "Any autosomal agammaglobulinemia in which the cause of the disease is a mutation in the CD79B gene." }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "CD79B autosomal agammaglobulinemia", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "autosomal agammaglobulinemia caused by mutation in CD79B", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "AGM6", "description": "" }, { "id": "MIM:612692", "resource": "MIM", "url": "https://www.omim.org/entry/612692", "name": "Agammaglobulinemia 6, autosomal recessive", "description": "Agammaglobulinemia 6, autosomal recessive" } ], "unlinked_id_list": [], "evidence": [ { "id": "612692", "database": "MIM", "url": "https://www.omim.org/entry/612692" }, { "id": "0081138", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0081138" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40259-1.127.127", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40259-1.128.128", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40259-1.129.129", "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": "P40259-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P40259", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MARLALSPVPSHWMV", "down_seq": "LLLLLSAEPVPAARSEDRYR", "snv": [ { "evidence": [ { "id": "P40259", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259" } ], "glycoeffect": [], "subjects_tested": "1704", "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": "63932215", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A16", "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: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": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40259-1.0.0", "categories": [ "biomarkers_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40259-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757407417", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757407417", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757407417", "url": "https://www.ensembl.org/id/rs757407417", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IIVPIFLLLDKDDSKAGMEE", "down_seq": "HTYEGLDIDQTATYEDIVTL", "snv": [ { "evidence": [ { "id": "rs757407417", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757407417" }, { "id": "rs757407417", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs757407417" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DHT->NHT).", "chr_id": "17", "chr_pos": "63929448", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D193", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P40259-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40259-1.207.207", "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": "P40259-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs912718113", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs912718113", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs912718113", "url": "https://www.ncbi.nlm.nih.gov/snp/rs912718113#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs912718113", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs912718113", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PRFIARKRGFTVKMHCYMNS", "down_seq": "SGNVSWLWKQEMDENPQQLK", "snv": [ { "evidence": [ { "id": "rs912718113", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs912718113" }, { "id": "rs912718113", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs912718113#frequency_tab" }, { "id": "rs912718113", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs912718113" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSA->NST).", "chr_id": "17", "chr_pos": "63930296", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A70", "disease": [ { "disease_id": "DOID:0081138", "recommended_name": { "id": "DOID:0081138", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0081138", "name": "agammaglobulinemia 6", "description": "An agammaglobulinemia that has_material_basis_in homozygous mutation in the CD79B gene on chromosome 17q23." }, "synonyms": [ { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "Any autosomal agammaglobulinemia in which the cause of the disease is a mutation in the CD79B gene." }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "CD79B autosomal agammaglobulinemia", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "agammaglobulinemia 6, autosomal recessive", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "autosomal agammaglobulinemia caused by mutation in CD79B", "description": "" }, { "id": "MONDO:0012987", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012987", "name": "AGM6", "description": "" }, { "id": "MIM:612692", "resource": "MIM", "url": "https://www.omim.org/entry/612692", "name": "Agammaglobulinemia 6, autosomal recessive", "description": "Agammaglobulinemia 6, autosomal recessive" } ], "unlinked_id_list": [], "evidence": [ { "id": "612692", "database": "MIM", "url": "https://www.omim.org/entry/612692" }, { "id": "0081138", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0081138" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40259-1.55.57", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40259-1.68.68", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40259-1.73.73", "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": "P40259-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P40259", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "WKQEMDENPQQLKLEKGRME", "down_seq": "SQNESLATLTIQGIRFEDNG", "snv": [ { "evidence": [ { "id": "P40259", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P40259" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "63930215", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E98", "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": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P40259-1.101.101", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40259-1.106.106", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40259-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Activation and serine phosphorylation of the p56lck protein tyrosine kinase in response to antigen receptor cross-linking in B lymphocytes.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "1994", "authors": "Gold MR, Chiu R, Ingham RJ, Saxton TM, van Oostveen I, Watts JD, Affolter M, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P40259-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259-1" } ], "reference": [ { "type": "PubMed", "id": "8077654", "url": "https://glygen.org/publication/PubMed/8077654" } ] }, { "title": "Asymmetrical phosphorylation and function of immunoreceptor tyrosine-based activation motif tyrosines in B cell antigen receptor signal transduction.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "1998", "authors": "Pao LI, Famiglietti SJ, Cambier JC", "evidence": [ { "database": "iPTMnet", "id": "P40259-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259-1" } ], "reference": [ { "type": "PubMed", "id": "9531288", "url": "https://glygen.org/publication/PubMed/9531288" } ] }, { "title": "Reconstitution of the B cell antigen receptor signaling components in COS cells.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Saouaf SJ, Kut SA, Fargnoli J, Rowley RB, Bolen JB, Mahajan S", "evidence": [ { "database": "Reactome", "id": "R-HSA-983695", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-983695" }, { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" } ], "reference": [ { "type": "PubMed", "id": "7592958", "url": "https://glygen.org/publication/PubMed/7592958" } ] }, { "title": "Tyrosine phosphorylation within the intrinsically disordered cytosolic domains of the B-cell receptor: an NMR-based structural analysis.", "journal": "PloS one", "date": "2014", "authors": "Rosenlow J, Isaksson L, Mayzel M, Lengqvist J, Orekhov VY", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" } ], "reference": [ { "type": "PubMed", "id": "24769851", "url": "https://glygen.org/publication/PubMed/24769851" } ] } ], "crossref": [ { "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "8077654", "url": "https://glygen.org/publication/PubMed/8077654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9531288", "url": "https://glygen.org/publication/PubMed/9531288", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7592958", "url": "https://glygen.org/publication/PubMed/7592958", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P40259", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P40259", "database": "PRO", "categories": [ "Other" ] }, { "id": "24769851", "url": "https://glygen.org/publication/PubMed/24769851", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PIFLLLDKDDSKAGMEEDHT", "down_seq": "EGLDIDQTATYEDIVTLRTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06239-1", "kinase_gene_name": "LCK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "8077654", "url": "https://glygen.org/publication/PubMed/8077654" } ], "site_lbl": "Tyr196" }, { "kinase_uniprot_canonical_ac": "P06241-1", "kinase_gene_name": "FYN", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "9531288", "url": "https://glygen.org/publication/PubMed/9531288" } ], "site_lbl": "Tyr196" }, { "kinase_uniprot_canonical_ac": "P07948-1", "kinase_gene_name": "LYN", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "9531288", "url": "https://glygen.org/publication/PubMed/9531288" } ], "site_lbl": "Tyr196" }, { "kinase_uniprot_canonical_ac": "P51451-1", "kinase_gene_name": "BLK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "7592958", "url": "https://glygen.org/publication/PubMed/7592958" } ], "site_lbl": "Tyr196" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by SRC-type Tyr-kinases", "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" }, { "database": "PRO", "id": "P40259", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P40259" }, { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "24769851", "url": "https://glygen.org/publication/PubMed/24769851" } ], "site_lbl": "Tyr196" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40259-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40259-1.207.207", "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": 5 } ], "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": "P40259-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Activation and serine phosphorylation of the p56lck protein tyrosine kinase in response to antigen receptor cross-linking in B lymphocytes.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "1994", "authors": "Gold MR, Chiu R, Ingham RJ, Saxton TM, van Oostveen I, Watts JD, Affolter M, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P40259-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259-1" } ], "reference": [ { "type": "PubMed", "id": "8077654", "url": "https://glygen.org/publication/PubMed/8077654" } ] }, { "title": "Asymmetrical phosphorylation and function of immunoreceptor tyrosine-based activation motif tyrosines in B cell antigen receptor signal transduction.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "1998", "authors": "Pao LI, Famiglietti SJ, Cambier JC", "evidence": [ { "database": "iPTMnet", "id": "P40259-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259-1" } ], "reference": [ { "type": "PubMed", "id": "9531288", "url": "https://glygen.org/publication/PubMed/9531288" } ] }, { "title": "Reconstitution of the B cell antigen receptor signaling components in COS cells.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Saouaf SJ, Kut SA, Fargnoli J, Rowley RB, Bolen JB, Mahajan S", "evidence": [ { "database": "Reactome", "id": "R-HSA-983695", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-983695" }, { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" } ], "reference": [ { "type": "PubMed", "id": "7592958", "url": "https://glygen.org/publication/PubMed/7592958" } ] }, { "title": "Tyrosine phosphorylation within the intrinsically disordered cytosolic domains of the B-cell receptor: an NMR-based structural analysis.", "journal": "PloS one", "date": "2014", "authors": "Rosenlow J, Isaksson L, Mayzel M, Lengqvist J, Orekhov VY", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" } ], "reference": [ { "type": "PubMed", "id": "24769851", "url": "https://glygen.org/publication/PubMed/24769851" } ] } ], "crossref": [ { "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "8077654", "url": "https://glygen.org/publication/PubMed/8077654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9531288", "url": "https://glygen.org/publication/PubMed/9531288", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7592958", "url": "https://glygen.org/publication/PubMed/7592958", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P40259", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P40259", "database": "PRO", "categories": [ "Other" ] }, { "id": "24769851", "url": "https://glygen.org/publication/PubMed/24769851", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KAGMEEDHTYEGLDIDQTAT", "down_seq": "EDIVTLRTGEVKWSVGEHPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06239-1", "kinase_gene_name": "LCK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "8077654", "url": "https://glygen.org/publication/PubMed/8077654" } ], "site_lbl": "Tyr207" }, { "kinase_uniprot_canonical_ac": "P06241-1", "kinase_gene_name": "FYN", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "9531288", "url": "https://glygen.org/publication/PubMed/9531288" } ], "site_lbl": "Tyr207" }, { "kinase_uniprot_canonical_ac": "P07948-1", "kinase_gene_name": "LYN", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "9531288", "url": "https://glygen.org/publication/PubMed/9531288" } ], "site_lbl": "Tyr207" }, { "kinase_uniprot_canonical_ac": "P51451-1", "kinase_gene_name": "BLK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "7592958", "url": "https://glygen.org/publication/PubMed/7592958" } ], "site_lbl": "Tyr207" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by SRC-type Tyr-kinases", "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" }, { "database": "PRO", "id": "P40259", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P40259" }, { "database": "iPTMnet", "id": "P40259", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40259" }, { "database": "PubMed", "id": "24769851", "url": "https://glygen.org/publication/PubMed/24769851" } ], "site_lbl": "Tyr207" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40259-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40259-1.196.196", "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": 5 } ], "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": "P40259-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P40259-1", "length": 229, "uniprot_id": "CD79B_HUMAN", "protein_name": "B-cell antigen receptor complex-associated protein beta chain", "refseq_ac": "NP_000617", "refseq_name": "B-cell antigen receptor complex-associated protein beta chain isoform 1 precursor", "gene_name": "CD79B", "gene_names_uniprotkb": "CD79B; B29; IGB", "gene_names_refseq": "AGM6; B29; CD79B; IGB; Igbeta", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P40259", "url": "https://www.uniprot.org/uniprotkb/P40259" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "BB3849-1", "url": "https://biomarkerkb.org/biomarker/BB3849-1", "database": "BiomarkerKB", "categories": [ "Biomarkers" ] }, { "id": "39947417", "url": "", "database": "PubMed", "categories": [ "Other" ] } ], "biomarkers": [ { "biomarker_id": "BB3849-1", "biomarker_canonical_id": "BB3849", "best_biomarker_role": [ "" ], "condition": { "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." }, "name_list": [ "ovarian cancer", "malignant Ovarian tumor", "malignant tumour of ovary", "ovarian neoplasm", "ovary neoplasm", "primary ovarian cancer", "tumor of the Ovary", "tumor of the ovary", "tumour of the ovary", "cancer of ovary", "cancer of the ovary", "malignant neoplasm of ovary", "malignant neoplasm of the ovary", "malignant ovarian neoplasm", "malignant ovarian tumor", "malignant ovarian tumour", "malignant ovary neoplasm", "malignant tumor of ovary", "malignant tumor of the ovary", "malignant tumour of the ovary", "ovarian cancer, somatic", "ovarian malignant tumor", "ovarian malignant tumour", "ovary cancer", "ovarian cancer, susceptibility to, 1", "OVCAS1", "ovarian cancer, susceptibility to", "Ovarian cancer" ], "id_list": [ "DOID:2394", "MONDO:0008170", "MONDO:0011931", "MIM:167000" ] }, "evidence": [ { "id": "BB3849-1", "database": "BiomarkerKB", "url": "https://biomarkerkb.org/biomarker/BB3849-1" }, { "id": "39947417", "database": "PubMed", "url": "" } ], "assessed_biomarker_entity": [ "B-cell antigen receptor complex-associated protein beta chain" ], "biomarker": [ "decreased level of Le^y on immunoglobulin M" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "73", "end_pos": "73" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "55", "end_pos": "57" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "biomarkers_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P40259-1.16.16", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SEEVVQKMTGLKVPLSHSRS", "down_seq": "DTLYIPEWEGRAPDSVDYRK", "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": "Asn103", "evidence": [ { "id": "P43235", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P43235#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 19, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.123.123", "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": "P43235-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1226682505", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226682505", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1226682505", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1226682505", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RAPDSVDYRKKGYVTPVKNQ", "down_seq": "QCGSCWAFSSVGALEGQLKK", "snv": [ { "evidence": [ { "id": "rs1226682505", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226682505" }, { "id": "rs1226682505", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1226682505" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NQG->NQS); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804239", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G134", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654044085", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654044085", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654044085", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654044085#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752495829", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752495829", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752495829", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752495829", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752495829", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752495829", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1175449258", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1175449258", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1175449258", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1175449258", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GQCGSCWAFSSVGALEGQLK", "down_seq": "KTGKLLNLSPQNLVDCVSEN", "snv": [ { "evidence": [ { "id": "rs1654044085", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654044085" }, { "id": "rs1654044085", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654044085#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (KKT->NKT); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804177", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K154", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs752495829", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752495829" }, { "id": "rs752495829", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752495829" }, { "id": "rs752495829", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752495829" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804179", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K154", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1175449258", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1175449258" }, { "id": "rs1175449258", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1175449258" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804178", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K154", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525173667", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173667", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1255952340", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1255952340", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1255952340", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1255952340", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2525173663", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173663", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "NDGCGGGYMTNAFQYVQKNR", "down_seq": "IDSEDAYPYVGQEESCMYNP", "snv": [ { "evidence": [ { "id": "rs2525173667", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173667" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NRG->NRS); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804059", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G194", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1255952340", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1255952340" }, { "id": "rs1255952340", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1255952340" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804058", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G194", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1255952340", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1255952340" }, { "id": "rs1255952340", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1255952340" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804058", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G194", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2525173663", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173663" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804061", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G194", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.214.214", "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": 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": "P43235-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654040870", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654040870", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654040870", "url": "https://www.ensembl.org/id/rs1654040870", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2525166951", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166951", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GIDSEDAYPYVGQEESCMYN", "down_seq": "TGKAAKCRGYREIPEGNEKA", "snv": [ { "evidence": [ { "id": "rs1654040870", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654040870" }, { "id": "rs1654040870", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654040870" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NPT->NAT); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804035", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P214", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2525166951", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166951" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NPT->NLT); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799687", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P214", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.234.234", "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": 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": "P43235-1.233.233", "start_pos": 233, "end_pos": 233, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1426414496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1426414496", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1426414496", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1426414496#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1426414496", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1426414496", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2525166556", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166556", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NPTGKAAKCRGYREIPEGNE", "down_seq": "ALKRAVARVGPVSVAIDASL", "snv": [ { "evidence": [ { "id": "rs1426414496", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1426414496" }, { "id": "rs1426414496", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1426414496#frequency_tab" }, { "id": "rs1426414496", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1426414496" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NEK->NET); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799630", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K233", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2525166556", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166556" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799631TC", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K233", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs770343722", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770343722", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770343722", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770343722", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GNEKALKRAVARVGPVSVAI", "down_seq": "ASLTSFQFYSKGVYYDESCN", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: n-glyco-sequon-gain (DAS->NAS); protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799580", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D250", "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": "rs770343722", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770343722" }, { "id": "rs770343722", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770343722" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799579", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D250", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.270.270", "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": 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": "P43235-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1571123597", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571123597", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571123597", "url": "https://www.ensembl.org/id/rs1571123597", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EKALKRAVARVGPVSVAIDA", "down_seq": "LTSFQFYSKGVYYDESCNSD", "snv": [ { "evidence": [ { "id": "rs1571123597", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571123597" }, { "id": "rs1571123597", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1571123597" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (SLT->NLT); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799573", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S252", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1571123597", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571123597" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799573", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S252", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.272.272", "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": 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": "P43235-1.266.266", "start_pos": 266, "end_pos": 266, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1332783199", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1332783199", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1332783199", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1332783199#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1332783199", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1332783199", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SVAIDASLTSFQFYSKGVYY", "down_seq": "ESCNSDNLNHAVLAVGYGIQ", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: n-glyco-sequon-gain (DES->NES); protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799262", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D266", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1332783199", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1332783199" }, { "id": "rs1332783199", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1332783199#frequency_tab" }, { "id": "rs1332783199", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1332783199" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799262", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D266", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KNSWGENWGNKGYILMARNK", "down_seq": "NACGIANLASFPKM", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 2 filters: n-glyco-sequon-gain (NKN->NKS); protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796845", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N315", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.329.329", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.317.317", "start_pos": 317, "end_pos": 317, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs587756638", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587756638", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs587756638", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587756638", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs587756638", "url": "https://www.ncbi.nlm.nih.gov/snp/rs587756638#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs587756638", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587756638", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1653884829", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653884829", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653884829", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653884829#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SWGENWGNKGYILMARNKNN", "down_seq": "CGIANLASFPKM", "snv": [ { "evidence": [ { "id": "rs587756638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587756638" }, { "id": "rs587756638", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587756638" }, { "id": "rs587756638", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs587756638#frequency_tab" }, { "id": "rs587756638", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587756638" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NNA->NNT); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796840", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A317", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1653884829", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653884829" }, { "id": "rs1653884829", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653884829#frequency_tab" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796839", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A317", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1653884829", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653884829" }, { "id": "rs1653884829", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653884829#frequency_tab" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150796839", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A317", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.324.324", "start_pos": 324, "end_pos": 324, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2525161781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525161781", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NKGYILMARNKNNACGIANL", "down_seq": "SFPKM", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 2 filters: n-glyco-sequon-gain (NLA->NLS); protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796819", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A324", "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": "rs2525161781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525161781" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NLA->NLT); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796819", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A324", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs995485377", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs995485377", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs995485377", "url": "https://www.ncbi.nlm.nih.gov/snp/rs995485377#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs995485377", "url": "http://gnomad.broadinstitute.org/awesome?query=rs995485377", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1340266187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1340266187", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1340266187", "url": "https://www.ensembl.org/id/rs1340266187", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HNLEASLGVHTYELAMNHLG", "down_seq": "MTSEEVVQKMTGLKVPLSHS", "snv": [ { "evidence": [ { "id": "rs995485377", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs995485377" }, { "id": "rs995485377", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs995485377#frequency_tab" }, { "id": "rs995485377", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs995485377" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (DMT->NMT); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806107", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D80", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1340266187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1340266187" }, { "id": "rs1340266187", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1340266187" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806106", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D80", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs995485377", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs995485377" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806107", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D80", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.100.100", "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": 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": "P43235-1.89.89", "start_pos": 89, "end_pos": 89, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654084140", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654084140", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654084140", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654084140#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HTYELAMNHLGDMTSEEVVQ", "down_seq": "MTGLKVPLSHSRSNDTLYIP", "snv": [ { "evidence": [ { "id": "rs1654084140", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654084140" }, { "id": "rs1654084140", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654084140#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (KMT->NMT); glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805993", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K89", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1284006847", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284006847", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1284006847", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1284006847#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1284006847", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1284006847", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DMTSEEVVQKMTGLKVPLSH", "down_seq": "RSNDTLYIPEWEGRAPDSVD", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150805962", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S100", "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": "rs1284006847", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284006847" }, { "id": "rs1284006847", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1284006847#frequency_tab" }, { "id": "rs1284006847", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1284006847" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805961", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S100", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.120.120", "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": 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": "P43235-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs780461752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780461752", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780461752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780461752", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780461752", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780461752#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780461752", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780461752", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200742781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200742781", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200742781", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200742781", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200742781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200742781", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200742781", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200742781#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200742781", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200742781", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MTSEEVVQKMTGLKVPLSHS", "down_seq": "SNDTLYIPEWEGRAPDSVDY", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs780461752", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780461752" }, { "id": "rs780461752", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780461752" }, { "id": "rs780461752", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780461752#frequency_tab" }, { "id": "rs780461752", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780461752" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805959", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R101", "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", "ebi", "germline" ] }, { "evidence": [ { "id": "rs200742781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200742781" }, { "id": "rs200742781", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200742781" }, { "id": "rs200742781", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200742781" }, { "id": "rs200742781", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200742781#frequency_tab" }, { "id": "rs200742781", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200742781" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805958", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R101", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200742781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200742781" }, { "id": "rs200742781", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200742781" }, { "id": "rs200742781", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200742781" }, { "id": "rs200742781", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200742781#frequency_tab" }, { "id": "rs200742781", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200742781" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805958", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R101", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746005364", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746005364", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746005364", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746005364", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746005364", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746005364", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSEEVVQKMTGLKVPLSHSR", "down_seq": "NDTLYIPEWEGRAPDSVDYR", "snv": [ { "evidence": [ { "id": "rs746005364", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746005364" }, { "id": "rs746005364", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746005364" }, { "id": "rs746005364", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746005364" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805955", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S102", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.122.122", "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": "P43235-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101953255", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953255", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953255", "url": "https://www.ensembl.org/id/rs2101953255", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EEVVQKMTGLKVPLSHSRSN", "down_seq": "TLYIPEWEGRAPDSVDYRKK", "snv": [ { "evidence": [ { "id": "rs2101953255", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953255" }, { "id": "rs2101953255", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953255" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805950", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D104", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.123.123", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EVVQKMTGLKVPLSHSRSND", "down_seq": "LYIPEWEGRAPDSVDYRKKG", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805946", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T105", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654082136", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654082136", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654082136", "url": "https://www.ensembl.org/id/rs1654082136", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1282841642", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1282841642", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1282841642", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1282841642", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654082278", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654082278", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654082278", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654082278", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VQKMTGLKVPLSHSRSNDTL", "down_seq": "IPEWEGRAPDSVDYRKKGYV", "snv": [ { "evidence": [ { "id": "rs1654082136", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654082136" }, { "id": "rs1654082136", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654082136" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805939", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y107", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1282841642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1282841642" }, { "id": "rs1282841642", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1282841642" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805940", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y107", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654082278", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654082278" }, { "id": "rs1654082278", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654082278" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805941", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y107", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.127.127", "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": 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": "P43235-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs137874306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137874306", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs137874306", "url": "https://www.ncbi.nlm.nih.gov/snp/rs137874306#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs137874306", "url": "http://gnomad.broadinstitute.org/awesome?query=rs137874306", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "QKMTGLKVPLSHSRSNDTLY", "down_seq": "PEWEGRAPDSVDYRKKGYVT", "snv": [ { "evidence": [ { "id": "rs137874306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137874306" }, { "id": "rs137874306", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs137874306#frequency_tab" }, { "id": "rs137874306", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs137874306" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805938", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I108", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs137874306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137874306" }, { "id": "rs137874306", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs137874306#frequency_tab" }, { "id": "rs137874306", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs137874306" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805938", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I108", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.128.128", "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": 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": "P43235-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KMTGLKVPLSHSRSNDTLYI", "down_seq": "EWEGRAPDSVDYRKKGYVTP", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805935", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P109", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.128.128", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654101066", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654101066", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654101066", "url": "https://www.ensembl.org/id/rs1654101066", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MWGLKVLLL", "down_seq": "VVSFALYPEEILDTHWELWK", "snv": [ { "evidence": [ { "id": "rs1654101066", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654101066" }, { "id": "rs1654101066", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654101066" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806778", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P10", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806777", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P10", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.30.30", "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": [ "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": "P43235-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2101953230", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953230", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953230", "url": "https://www.ensembl.org/id/rs2101953230", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MTGLKVPLSHSRSNDTLYIP", "down_seq": "WEGRAPDSVDYRKKGYVTPV", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805932", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E110", "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": "rs2101953230", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953230" }, { "id": "rs2101953230", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953230" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805930", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E110", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.130.130", "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": 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": "P43235-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1327487985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1327487985", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1327487985", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1327487985", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "TGLKVPLSHSRSNDTLYIPE", "down_seq": "EGRAPDSVDYRKKGYVTPVK", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805927", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "W111", "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": "rs1327487985", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1327487985" }, { "id": "rs1327487985", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1327487985" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805929", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W111", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.130.130", "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": 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": "P43235-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs587775407", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587775407", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs587775407", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587775407", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs587775407", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587775407", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs587775407", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587775407", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GLKVPLSHSRSNDTLYIPEW", "down_seq": "GRAPDSVDYRKKGYVTPVKN", "snv": [ { "evidence": [ { "id": "rs587775407", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587775407" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805926", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E112", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs587775407", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587775407" }, { "id": "rs587775407", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587775407" }, { "id": "rs587775407", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587775407" }, { "id": "rs587775407", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587775407" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805926", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "E112", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs587775407", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587775407" }, { "id": "rs587775407", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587775407" }, { "id": "rs587775407", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587775407" }, { "id": "rs587775407", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587775407" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805926", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "E112", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.132.132", "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": 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": "P43235-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753591279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753591279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753591279", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753591279#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753591279", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753591279", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LKVPLSHSRSNDTLYIPEWE", "down_seq": "RAPDSVDYRKKGYVTPVKNQ", "snv": [ { "evidence": [ { "id": "rs753591279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279" }, { "id": "rs753591279", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279" }, { "id": "rs753591279", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753591279#frequency_tab" }, { "id": "rs753591279", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753591279" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805922", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G113", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753591279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279" }, { "id": "rs753591279", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279" }, { "id": "rs753591279", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753591279#frequency_tab" }, { "id": "rs753591279", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753591279" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805922", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G113", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.133.133", "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": "P43235-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs772730842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772730842", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772730842", "url": "https://www.ensembl.org/id/rs772730842", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KVPLSHSRSNDTLYIPEWEG", "down_seq": "APDSVDYRKKGYVTPVKNQG", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs772730842", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772730842" }, { "id": "rs772730842", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs772730842" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150805919", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R114", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1457219593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1457219593", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1457219593", "url": "https://www.ensembl.org/id/rs1457219593", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VPLSHSRSNDTLYIPEWEGR", "down_seq": "PDSVDYRKKGYVTPVKNQGQ", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1457219593", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1457219593" }, { "id": "rs1457219593", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1457219593" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805917", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A115", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.135.135", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777647239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777647239", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777647239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777647239", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777647239", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777647239#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777647239", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777647239", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PLSHSRSNDTLYIPEWEGRA", "down_seq": "DSVDYRKKGYVTPVKNQGQC", "snv": [ { "evidence": [ { "id": "rs777647239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777647239" }, { "id": "rs777647239", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777647239" }, { "id": "rs777647239", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777647239#frequency_tab" }, { "id": "rs777647239", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777647239" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805914", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs777647239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777647239" }, { "id": "rs777647239", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777647239" }, { "id": "rs777647239", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777647239#frequency_tab" }, { "id": "rs777647239", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777647239" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805914", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P116", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.136.136", "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": 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": "P43235-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1196352244", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1196352244", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1196352244", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1196352244#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1196352244", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1196352244", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LSHSRSNDTLYIPEWEGRAP", "down_seq": "SVDYRKKGYVTPVKNQGQCG", "snv": [ { "evidence": [ { "id": "rs1196352244", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1196352244" }, { "id": "rs1196352244", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1196352244#frequency_tab" }, { "id": "rs1196352244", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1196352244" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805911", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D117", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.137.137", "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": "P43235-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs752649562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752649562", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752649562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752649562", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752649562", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752649562#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752649562", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752649562", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SRSNDTLYIPEWEGRAPDSV", "down_seq": "YRKKGYVTPVKNQGQCGSCW", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805902", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D120", "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": "rs752649562", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752649562" }, { "id": "rs752649562", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752649562" }, { "id": "rs752649562", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752649562#frequency_tab" }, { "id": "rs752649562", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752649562" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805902", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D120", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150805902", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D120", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.140.140", "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": 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": "P43235-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1054278735", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1054278735", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1054278735", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1054278735#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1054278735", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1054278735", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2101953187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953187", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953187", "url": "https://www.ensembl.org/id/rs2101953187", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RSNDTLYIPEWEGRAPDSVD", "down_seq": "RKKGYVTPVKNQGQCGSCWA", "snv": [ { "evidence": [ { "id": "rs1054278735", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1054278735" }, { "id": "rs1054278735", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1054278735#frequency_tab" }, { "id": "rs1054278735", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1054278735" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805898", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y121", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101953187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953187" }, { "id": "rs2101953187", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953187" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805899", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y121", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.140.140", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "P43235-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs759107967", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759107967", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759107967", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759107967", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759107967", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759107967", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1553197383", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553197383", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1553197383", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1553197383", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SNDTLYIPEWEGRAPDSVDY", "down_seq": "KKGYVTPVKNQGQCGSCWAF", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs759107967", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759107967" }, { "id": "rs759107967", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759107967" }, { "id": "rs759107967", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759107967" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805896", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R122", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1553197383", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553197383" }, { "id": "rs1553197383", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1553197383" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805895", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R122", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NDTLYIPEWEGRAPDSVDYR", "down_seq": "KGYVTPVKNQGQCGSCWAFS", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805891", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K123", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753591279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753591279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753591279", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753591279#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753591279", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753591279", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TLYIPEWEGRAPDSVDYRKK", "down_seq": "YVTPVKNQGQCGSCWAFSSV", "snv": [ { "evidence": [ { "id": "rs753591279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279" }, { "id": "rs753591279", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279" }, { "id": "rs753591279", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753591279#frequency_tab" }, { "id": "rs753591279", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753591279" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805922", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G125", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753591279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279" }, { "id": "rs753591279", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753591279" }, { "id": "rs753591279", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753591279#frequency_tab" }, { "id": "rs753591279", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753591279" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805922", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G125", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.144.144", "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": 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": "P43235-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101953162", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953162", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LYIPEWEGRAPDSVDYRKKG", "down_seq": "VTPVKNQGQCGSCWAFSSVG", "snv": [ { "evidence": [ { "id": "rs2101953162", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953162" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805882AT", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y126", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.146.146", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1654080052", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654080052", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654080052", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654080052", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "YIPEWEGRAPDSVDYRKKGY", "down_seq": "TPVKNQGQCGSCWAFSSVGA", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805880", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "V127", "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": "rs1654080052", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654080052" }, { "id": "rs1654080052", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654080052" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805881", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V127", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.146.146", "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": 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": "P43235-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2101953152", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953152", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953152", "url": "https://www.ensembl.org/id/rs2101953152", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IPEWEGRAPDSVDYRKKGYV", "down_seq": "PVKNQGQCGSCWAFSSVGAL", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs2101953152", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953152" }, { "id": "rs2101953152", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953152" } ], "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: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805877", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T128", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.148.148", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654079940", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654079940", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EWEGRAPDSVDYRKKGYVTP", "down_seq": "KNQGQCGSCWAFSSVGALEG", "snv": [ { "evidence": [ { "id": "rs1654079940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654079940" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805877_150805962", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V130", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.150.150", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201308534", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201308534", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201308534", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201308534", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1057516725", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516725", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EGRAPDSVDYRKKGYVTPVK", "down_seq": "QGQCGSCWAFSSVGALEGQL", "snv": [ { "evidence": [ { "id": "rs201308534", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201308534" }, { "id": "rs201308534", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201308534" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805866", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N132", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1057516725", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516725" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805869", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N132", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.152.152", "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": 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": "P43235-1.133.133", "start_pos": 133, "end_pos": 133, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654079662", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654079662", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654079662", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654079662#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "GRAPDSVDYRKKGYVTPVKN", "down_seq": "GQCGSCWAFSSVGALEGQLK", "snv": [ { "evidence": [ { "id": "rs1654079662", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654079662" }, { "id": "rs1654079662", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654079662#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805863", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q133", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805863", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "Q133", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.153.153", "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": 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": 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": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2101951682", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951682", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "APDSVDYRKKGYVTPVKNQG", "down_seq": "CGSCWAFSSVGALEGQLKKK", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804236", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q135", "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": "rs2101951682", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951682" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804237", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q135", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200313416", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200313416", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200313416", "url": "https://www.ensembl.org/id/rs200313416", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "PDSVDYRKKGYVTPVKNQGQ", "down_seq": "GSCWAFSSVGALEGQLKKKT", "snv": [ { "evidence": [ { "id": "rs200313416", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200313416" }, { "id": "rs200313416", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs200313416" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804231", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C136", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1304816655", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1304816655", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1304816655", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1304816655#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1304816655", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1304816655", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DSVDYRKKGYVTPVKNQGQC", "down_seq": "SCWAFSSVGALEGQLKKKTG", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804230", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "G137", "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" ] }, { "evidence": [ { "id": "rs1304816655", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1304816655" }, { "id": "rs1304816655", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1304816655#frequency_tab" }, { "id": "rs1304816655", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1304816655" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804230", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G137", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs777898190", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777898190", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777898190", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777898190", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777898190", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777898190", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVDYRKKGYVTPVKNQGQCG", "down_seq": "CWAFSSVGALEGQLKKKTGK", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804226", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S138", "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": "rs777898190", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777898190" }, { "id": "rs777898190", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777898190" }, { "id": "rs777898190", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777898190" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804227", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S138", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.158.158", "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": 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": "P43235-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525174048", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525174048", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "VDYRKKGYVTPVKNQGQCGS", "down_seq": "WAFSSVGALEGQLKKKTGKL", "snv": [ { "evidence": [ { "id": "rs2525174048", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525174048" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804222", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C139", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.159.159", "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": 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": "P43235-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2101951671", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951671", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101951671", "url": "https://www.ensembl.org/id/rs2101951671", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "DYRKKGYVTPVKNQGQCGSC", "down_seq": "AFSSVGALEGQLKKKTGKLL", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs2101951671", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951671" }, { "id": "rs2101951671", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101951671" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804219", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W140", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804220", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "W140", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.160.160", "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": 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": "P43235-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1328740486", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1328740486", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1328740486", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1328740486#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1328740486", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1328740486", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1057516627", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516627", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1057516514", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516514", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "RKKGYVTPVKNQGQCGSCWA", "down_seq": "SSVGALEGQLKKKTGKLLNL", "snv": [ { "evidence": [ { "id": "rs1328740486", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1328740486" }, { "id": "rs1328740486", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1328740486#frequency_tab" }, { "id": "rs1328740486", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1328740486" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804215", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F142", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1057516627", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516627" }, { "id": "rs1057516514", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516514" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804193_150804220", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F142", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1273879735", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1273879735", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1273879735", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1273879735", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2101951646", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951646", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101951641", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951641", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KGYVTPVKNQGQCGSCWAFS", "down_seq": "VGALEGQLKKKTGKLLNLSP", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1273879735", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1273879735" }, { "id": "rs1273879735", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1273879735" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150804208", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S144", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101951646", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951646" }, { "id": "rs2101951641", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951641" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804210", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S144", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.164.164", "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": 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": "P43235-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Pycnodysostosis, a lysosomal disease caused by cathepsin K deficiency.", "journal": "Science (New York, N.Y.)", "date": "1996", "authors": "Gelb BD, Shi GP, Chapman HA, Desnick RJ", "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" }, { "database": "dbSNP", "id": "rs74315302", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315302" }, { "database": "dbSNP", "id": "rs74315303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315303" } ], "reference": [ { "type": "PubMed", "id": "8703060", "url": "https://glygen.org/publication/PubMed/8703060" } ] } ], "crossref": [ { "id": "rs2101951629", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951629", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101951629", "url": "https://www.ensembl.org/id/rs2101951629", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs74315302", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315302", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs74315302", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315302#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs74315302", "url": "http://gnomad.broadinstitute.org/awesome?query=rs74315302", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "8703060", "url": "https://glygen.org/publication/PubMed/8703060", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1226682505", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226682505", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1226682505", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1226682505", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YVTPVKNQGQCGSCWAFSSV", "down_seq": "ALEGQLKKKTGKLLNLSPQN", "snv": [ { "evidence": [ { "id": "rs2101951629", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951629" }, { "id": "rs2101951629", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101951629" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804202", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G146", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs74315302", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315302" }, { "id": "rs74315302", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315302#frequency_tab" }, { "id": "rs74315302", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs74315302" }, { "id": "8703060", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8703060" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804203", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G146", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ] }, { "evidence": [ { "id": "rs1226682505", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226682505" }, { "id": "rs1226682505", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1226682505" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804239", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G146", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43235-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654044461", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654044461", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654044461", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654044461#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "TPVKNQGQCGSCWAFSSVGA", "down_seq": "EGQLKKKTGKLLNLSPQNLV", "snv": [ { "evidence": [ { "id": "rs1654044461", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654044461" }, { "id": "rs1654044461", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654044461#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804196", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L148", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.168.168", "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": "P43235-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs938267905", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs938267905", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs938267905", "url": "https://www.ncbi.nlm.nih.gov/snp/rs938267905#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs938267905", "url": "http://gnomad.broadinstitute.org/awesome?query=rs938267905", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1364706209", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1364706209", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1364706209", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1364706209#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1364706209", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1364706209", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2101954082", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101954082", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101954082", "url": "https://www.ensembl.org/id/rs2101954082", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MWGLKVLLLPVVS", "down_seq": "ALYPEEILDTHWELWKKTHR", "snv": [ { "evidence": [ { "id": "rs938267905", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs938267905" }, { "id": "rs938267905", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs938267905#frequency_tab" }, { "id": "rs938267905", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs938267905" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806765", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F14", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1364706209", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1364706209" }, { "id": "rs1364706209", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1364706209#frequency_tab" }, { "id": "rs1364706209", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1364706209" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806764", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F14", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101954082", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101954082" }, { "id": "rs2101954082", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101954082" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806766", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F14", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 13, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.34.34", "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": 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": "P43235-1.150.150", "start_pos": 150, "end_pos": 150, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1428904720", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1428904720", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1428904720", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1428904720", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VKNQGQCGSCWAFSSVGALE", "down_seq": "QLKKKTGKLLNLSPQNLVDC", "snv": [ { "evidence": [ { "id": "rs1428904720", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1428904720" }, { "id": "rs1428904720", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1428904720" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804191", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G150", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.170.170", "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": "P43235-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654044239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654044239", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654044239", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654044239#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NQGQCGSCWAFSSVGALEGQ", "down_seq": "KKKTGKLLNLSPQNLVDCVS", "snv": [ { "evidence": [ { "id": "rs1654044239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654044239" }, { "id": "rs1654044239", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654044239#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804185", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L152", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804185", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L152", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.172.172", "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", "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": "P43235-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525173966", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173966", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2101951608", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951608", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "QGQCGSCWAFSSVGALEGQL", "down_seq": "KKTGKLLNLSPQNLVDCVSE", "snv": [ { "evidence": [ { "id": "rs2525173966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173966" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804182", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K153", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804181", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K153", "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" ] }, { "evidence": [ { "id": "rs2101951608", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951608" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804182", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K153", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1557825913", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1557825913", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1557825913", "url": "https://www.ensembl.org/id/rs1557825913", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs761204120", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761204120", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761204120", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761204120", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761204120", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761204120#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs761204120", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761204120", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs587767484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587767484", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs587767484", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587767484", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs587767484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587767484", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs587767484", "url": "https://www.ncbi.nlm.nih.gov/snp/rs587767484#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs587767484", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587767484", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SCWAFSSVGALEGQLKKKTG", "down_seq": "LLNLSPQNLVDCVSENDGCG", "snv": [ { "evidence": [ { "id": "rs1557825913", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1557825913" }, { "id": "rs1557825913", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1557825913" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804167", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K158", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs761204120", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761204120" }, { "id": "rs761204120", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761204120" }, { "id": "rs761204120", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761204120#frequency_tab" }, { "id": "rs761204120", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761204120" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804165", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K158", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs587767484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587767484" }, { "id": "rs587767484", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587767484" }, { "id": "rs587767484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587767484" }, { "id": "rs587767484", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs587767484#frequency_tab" }, { "id": "rs587767484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587767484" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804166", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "K158", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs587767484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587767484" }, { "id": "rs587767484", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587767484" }, { "id": "rs587767484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587767484" }, { "id": "rs587767484", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs587767484#frequency_tab" }, { "id": "rs587767484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587767484" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804166", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "K158", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.178.178", "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": 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": "P43235-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525173940", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173940", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "CWAFSSVGALEGQLKKKTGK", "down_seq": "LNLSPQNLVDCVSENDGCGG", "snv": [ { "evidence": [ { "id": "rs2525173940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173940" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804163_150804164insCAATGATG", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L159", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.179.179", "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": 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": "P43235-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525180631", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180631", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MWGLKVLLLPVVSF", "down_seq": "LYPEEILDTHWELWKKTHRK", "snv": [ { "evidence": [ { "id": "rs2525180631", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180631" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806763", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A15", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 14, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1654044461", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654044461", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654044461", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654044461#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "WAFSSVGALEGQLKKKTGKL", "down_seq": "NLSPQNLVDCVSENDGCGGG", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804159", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L160", "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": "rs1654044461", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654044461" }, { "id": "rs1654044461", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654044461#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804196", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L160", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.179.179", "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": 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": "P43235-1.161.161", "start_pos": 161, "end_pos": 161, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1402899433", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402899433", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1402899433", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1402899433#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1402899433", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402899433", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs751076750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751076750", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751076750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751076750", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751076750", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751076750", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AFSSVGALEGQLKKKTGKLL", "down_seq": "LSPQNLVDCVSENDGCGGGY", "snv": [ { "evidence": [ { "id": "rs1402899433", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402899433" }, { "id": "rs1402899433", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1402899433#frequency_tab" }, { "id": "rs1402899433", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402899433" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804157", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N161", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804157", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N161", "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": "rs751076750", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751076750" }, { "id": "rs751076750", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751076750" }, { "id": "rs751076750", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751076750" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804158", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N161", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.181.181", "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": 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": "P43235-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "FSSVGALEGQLKKKTGKLLN", "down_seq": "SPQNLVDCVSENDGCGGGYM", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804155", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L162", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.181.181", "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": "P43235-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762590247", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762590247", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762590247", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762590247", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762590247", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762590247", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSVGALEGQLKKKTGKLLNL", "down_seq": "PQNLVDCVSENDGCGGGYMT", "snv": [ { "evidence": [ { "id": "rs762590247", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762590247" }, { "id": "rs762590247", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762590247" }, { "id": "rs762590247", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762590247" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804152", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S163", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804151", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S163", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.183.183", "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": 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": "P43235-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs886045274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886045274", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs886045274", "url": "https://www.ensembl.org/id/rs886045274", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SVGALEGQLKKKTGKLLNLS", "down_seq": "QNLVDCVSENDGCGGGYMTN", "snv": [ { "evidence": [ { "id": "rs886045274", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886045274" }, { "id": "rs886045274", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs886045274" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804149", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P164", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.184.184", "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": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs750083111", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750083111", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750083111", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750083111", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750083111", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750083111", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654043546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654043546", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "VGALEGQLKKKTGKLLNLSP", "down_seq": "NLVDCVSENDGCGGGYMTNA", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804146", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q165", "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": "rs750083111", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750083111" }, { "id": "rs750083111", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750083111" }, { "id": "rs750083111", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750083111" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804145", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q165", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654043546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654043546" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804149", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q165", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.185.185", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "P43235-1.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1281651602", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1281651602", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1281651602", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1281651602", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GALEGQLKKKTGKLLNLSPQ", "down_seq": "LVDCVSENDGCGGGYMTNAF", "snv": [ { "evidence": [ { "id": "rs1281651602", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1281651602" }, { "id": "rs1281651602", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1281651602" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804143", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N166", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.186.186", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1213730273", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1213730273", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1213730273", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1213730273#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1213730273", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1213730273", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "ALEGQLKKKTGKLLNLSPQN", "down_seq": "VDCVSENDGCGGGYMTNAFQ", "snv": [ { "evidence": [ { "id": "rs1213730273", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1213730273" }, { "id": "rs1213730273", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1213730273#frequency_tab" }, { "id": "rs1213730273", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1213730273" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804139", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L167", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1213730273", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1213730273" }, { "id": "rs1213730273", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1213730273#frequency_tab" }, { "id": "rs1213730273", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1213730273" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804139", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L167", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1309902734", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309902734", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1309902734", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309902734#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1309902734", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309902734", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LEGQLKKKTGKLLNLSPQNL", "down_seq": "DCVSENDGCGGGYMTNAFQY", "snv": [ { "evidence": [ { "id": "rs1309902734", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309902734" }, { "id": "rs1309902734", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309902734#frequency_tab" }, { "id": "rs1309902734", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309902734" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804136", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V168", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101951545", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951545", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101951545", "url": "https://www.ensembl.org/id/rs2101951545", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EGQLKKKTGKLLNLSPQNLV", "down_seq": "CVSENDGCGGGYMTNAFQYV", "snv": [ { "evidence": [ { "id": "rs2101951545", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951545" }, { "id": "rs2101951545", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101951545" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804134", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D169", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1474422274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1474422274", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1474422274", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1474422274", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MWGLKVLLLPVVSFA", "down_seq": "YPEEILDTHWELWKKTHRKQ", "snv": [ { "evidence": [ { "id": "rs1474422274", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1474422274" }, { "id": "rs1474422274", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1474422274" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806795", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L16", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 15, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1300052041", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1300052041", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1300052041", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1300052041", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "GQLKKKTGKLLNLSPQNLVD", "down_seq": "VSENDGCGGGYMTNAFQYVQ", "snv": [ { "evidence": [ { "id": "rs1300052041", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1300052041" }, { "id": "rs1300052041", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1300052041" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804130", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C170", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.190.190", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101951530", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951530", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101951530", "url": "https://www.ensembl.org/id/rs2101951530", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1654042998", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042998", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654042998", "url": "https://www.ensembl.org/id/rs1654042998", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKKKTGKLLNLSPQNLVDCV", "down_seq": "ENDGCGGGYMTNAFQYVQKN", "snv": [ { "evidence": [ { "id": "rs2101951530", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951530" }, { "id": "rs2101951530", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101951530" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804124", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S172", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804125", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S172", "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": "rs1654042998", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042998" }, { "id": "rs1654042998", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654042998" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804125", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S172", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.192.192", "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": 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": "P43235-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201315936", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201315936", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201315936", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201315936", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201315936", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201315936", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1345136673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1345136673", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1345136673", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1345136673#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KKKTGKLLNLSPQNLVDCVS", "down_seq": "NDGCGGGYMTNAFQYVQKNR", "snv": [ { "evidence": [ { "id": "rs201315936", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201315936" }, { "id": "rs201315936", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201315936" }, { "id": "rs201315936", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201315936" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804120", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E173", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1345136673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1345136673" }, { "id": "rs1345136673", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1345136673#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804122", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E173", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101951513", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951513", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101951513", "url": "https://www.ensembl.org/id/rs2101951513", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TGKLLNLSPQNLVDCVSEND", "down_seq": "CGGGYMTNAFQYVQKNRGID", "snv": [ { "evidence": [ { "id": "rs2101951513", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951513" }, { "id": "rs2101951513", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101951513" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804112", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G176", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101951513", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951513" }, { "id": "rs2101951513", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101951513" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804112", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G176", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.194.194", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "P43235-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781512523", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781512523", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "GKLLNLSPQNLVDCVSENDG", "down_seq": "GGGYMTNAFQYVQKNRGIDS", "snv": [ { "evidence": [ { "id": "rs781512523", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781512523" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804110", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C177", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.197.197", "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": "P43235-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760059010", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760059010", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760059010", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760059010", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760059010", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760059010#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760059010", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760059010", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs767971273", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767971273", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767971273", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767971273", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767971273", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767971273", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KLLNLSPQNLVDCVSENDGC", "down_seq": "GGYMTNAFQYVQKNRGIDSE", "snv": [ { "evidence": [ { "id": "rs760059010", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760059010" }, { "id": "rs760059010", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760059010" }, { "id": "rs760059010", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760059010#frequency_tab" }, { "id": "rs760059010", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760059010" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804106", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G178", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767971273", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767971273" }, { "id": "rs767971273", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767971273" }, { "id": "rs767971273", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767971273" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804107", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G178", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804106", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G178", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.197.197", "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": 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": "P43235-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200839013", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200839013", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200839013", "url": "https://www.ensembl.org/id/rs200839013", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LLNLSPQNLVDCVSENDGCG", "down_seq": "GYMTNAFQYVQKNRGIDSED", "snv": [ { "evidence": [ { "id": "rs200839013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200839013" }, { "id": "rs200839013", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs200839013" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804104", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G179", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.199.199", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1057516790", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516790", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MWGLKVLLLPVVSFAL", "down_seq": "PEEILDTHWELWKKTHRKQY", "snv": [ { "evidence": [ { "id": "rs1057516790", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516790" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806758", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y17", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 16, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs868112062", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868112062", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs868112062", "url": "https://www.ensembl.org/id/rs868112062", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1654042518", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042518", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654042518", "url": "https://www.ensembl.org/id/rs1654042518", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NLSPQNLVDCVSENDGCGGG", "down_seq": "MTNAFQYVQKNRGIDSEDAY", "snv": [ { "evidence": [ { "id": "rs868112062", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868112062" }, { "id": "rs868112062", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs868112062" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804098", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y181", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654042518", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042518" }, { "id": "rs1654042518", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654042518" } ], "glycoeffect": [], "sequence_org": "Y", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804097", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y181", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.201.201", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "P43235-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs949980727", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs949980727", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs949980727", "url": "https://www.ensembl.org/id/rs949980727", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1654042476", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042476", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654042476", "url": "https://www.ensembl.org/id/rs1654042476", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPQNLVDCVSENDGCGGGYM", "down_seq": "NAFQYVQKNRGIDSEDAYPY", "snv": [ { "evidence": [ { "id": "rs949980727", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs949980727" }, { "id": "rs949980727", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs949980727" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804091", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T183", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654042476", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042476" }, { "id": "rs1654042476", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654042476" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804092", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T183", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774888582", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774888582", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774888582", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774888582", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774888582", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774888582#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774888582", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774888582", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PQNLVDCVSENDGCGGGYMT", "down_seq": "AFQYVQKNRGIDSEDAYPYV", "snv": [ { "evidence": [ { "id": "rs774888582", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774888582" }, { "id": "rs774888582", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774888582" }, { "id": "rs774888582", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774888582#frequency_tab" }, { "id": "rs774888582", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774888582" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804088", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N184", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.204.204", "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": 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": "P43235-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1358531724", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1358531724", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1358531724", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1358531724", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QNLVDCVSENDGCGGGYMTN", "down_seq": "FQYVQKNRGIDSEDAYPYVG", "snv": [ { "evidence": [ { "id": "rs1358531724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1358531724" }, { "id": "rs1358531724", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1358531724" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804086", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A185", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101951483", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951483", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101951483", "url": "https://www.ensembl.org/id/rs2101951483", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "NLVDCVSENDGCGGGYMTNA", "down_seq": "QYVQKNRGIDSEDAYPYVGQ", "snv": [ { "evidence": [ { "id": "rs2101951483", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101951483" }, { "id": "rs2101951483", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101951483" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804083", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F186", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.206.206", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654042203", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042203", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654042203", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654042203#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776654874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776654874", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776654874", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776654874#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LVDCVSENDGCGGGYMTNAF", "down_seq": "YVQKNRGIDSEDAYPYVGQE", "snv": [ { "evidence": [ { "id": "rs1654042203", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042203" }, { "id": "rs1654042203", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654042203#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804080", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q187", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654042203", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654042203" }, { "id": "rs1654042203", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654042203#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804080", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q187", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776654874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776654874" }, { "id": "rs776654874", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776654874#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804079", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q187", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.206.206", "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": 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": "P43235-1.189.189", "start_pos": 189, "end_pos": 189, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200014002", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200014002", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200014002", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200014002", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200014002", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200014002", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "DCVSENDGCGGGYMTNAFQY", "down_seq": "QKNRGIDSEDAYPYVGQEES", "snv": [ { "evidence": [ { "id": "rs200014002", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200014002" }, { "id": "rs200014002", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200014002" }, { "id": "rs200014002", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200014002" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804073", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V189", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654099874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654099874", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654099874", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654099874#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1654099874", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654099874", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MWGLKVLLLPVVSFALY", "down_seq": "EEILDTHWELWKKTHRKQYN", "snv": [ { "evidence": [ { "id": "rs1654099874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654099874" }, { "id": "rs1654099874", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654099874#frequency_tab" }, { "id": "rs1654099874", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654099874" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806754", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P18", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654099874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654099874" }, { "id": "rs1654099874", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654099874#frequency_tab" }, { "id": "rs1654099874", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654099874" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806754", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P18", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 17, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.38.38", "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": 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": "P43235-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs202040269", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202040269", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202040269", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202040269", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs202040269", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202040269", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1180365957", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1180365957", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1180365957", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1180365957", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "CVSENDGCGGGYMTNAFQYV", "down_seq": "KNRGIDSEDAYPYVGQEESC", "snv": [ { "evidence": [ { "id": "rs202040269", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202040269" }, { "id": "rs202040269", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202040269" }, { "id": "rs202040269", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202040269" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804071", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q190", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1180365957", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1180365957" }, { "id": "rs1180365957", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1180365957" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804070", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q190", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VSENDGCGGGYMTNAFQYVQ", "down_seq": "NRGIDSEDAYPYVGQEESCM", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804066", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K191", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.211.211", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769923938", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769923938", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769923938", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769923938", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769923938", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769923938", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1553197239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553197239", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SENDGCGGGYMTNAFQYVQK", "down_seq": "RGIDSEDAYPYVGQEESCMY", "snv": [ { "evidence": [ { "id": "rs769923938", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769923938" }, { "id": "rs769923938", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769923938" }, { "id": "rs769923938", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769923938" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804065", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N192", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1553197239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553197239" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804062_150804063deli", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N192", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.212.212", "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": 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": "P43235-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747914097", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747914097", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747914097", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747914097", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747914097", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747914097#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747914097", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747914097", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs781168584", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781168584", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781168584", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781168584", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781168584", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781168584#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs781168584", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781168584", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ENDGCGGGYMTNAFQYVQKN", "down_seq": "GIDSEDAYPYVGQEESCMYN", "snv": [ { "evidence": [ { "id": "rs747914097", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747914097" }, { "id": "rs747914097", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747914097" }, { "id": "rs747914097", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747914097#frequency_tab" }, { "id": "rs747914097", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747914097" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804062", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R193", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs781168584", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781168584" }, { "id": "rs781168584", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781168584" }, { "id": "rs781168584", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781168584#frequency_tab" }, { "id": "rs781168584", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781168584" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804061", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R193", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs747914097", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747914097" }, { "id": "rs747914097", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747914097" }, { "id": "rs747914097", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747914097#frequency_tab" }, { "id": "rs747914097", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747914097" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804062", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R193", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.213.213", "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": 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": "P43235-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1271585034", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1271585034", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1271585034", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1271585034#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1271585034", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1271585034", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CGGGYMTNAFQYVQKNRGID", "down_seq": "EDAYPYVGQEESCMYNPTGK", "snv": [ { "evidence": [ { "id": "rs1271585034", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1271585034" }, { "id": "rs1271585034", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1271585034#frequency_tab" }, { "id": "rs1271585034", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1271585034" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804049", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S197", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.217.217", "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": "P43235-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200876016", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200876016", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200876016", "url": "https://www.ensembl.org/id/rs200876016", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GGYMTNAFQYVQKNRGIDSE", "down_seq": "AYPYVGQEESCMYNPTGKAA", "snv": [ { "evidence": [ { "id": "rs200876016", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200876016" }, { "id": "rs200876016", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs200876016" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804043", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D199", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.219.219", "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": "P43235-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654099778", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654099778", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654099778", "url": "https://www.ensembl.org/id/rs1654099778", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MWGLKVLLLPVVSFALYP", "down_seq": "EILDTHWELWKKTHRKQYNN", "snv": [ { "evidence": [ { "id": "rs1654099778", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654099778" }, { "id": "rs1654099778", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654099778" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806751", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E19", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.39.39", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.1.1", "start_pos": 1, "end_pos": 1, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525180749", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180749", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "", "down_seq": "WGLKVLLLPVVSFALYPEEI", "snv": [ { "evidence": [ { "id": "rs2525180749", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180749" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806805", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 1, "direction": "upstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754866059", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754866059", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754866059", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754866059", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754866059", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754866059#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754866059", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754866059", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GYMTNAFQYVQKNRGIDSED", "down_seq": "YPYVGQEESCMYNPTGKAAK", "snv": [ { "evidence": [ { "id": "rs754866059", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754866059" }, { "id": "rs754866059", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754866059" }, { "id": "rs754866059", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754866059#frequency_tab" }, { "id": "rs754866059", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754866059" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804041", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A200", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2525173632", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173632", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YMTNAFQYVQKNRGIDSEDA", "down_seq": "PYVGQEESCMYNPTGKAAKC", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804037", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "Y201", "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": "rs2525173632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525173632" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804040", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y201", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.221.221", "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": 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": "P43235-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654040870", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654040870", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654040870", "url": "https://www.ensembl.org/id/rs1654040870", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MTNAFQYVQKNRGIDSEDAY", "down_seq": "YVGQEESCMYNPTGKAAKCR", "snv": [ { "evidence": [ { "id": "rs1654040870", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654040870" }, { "id": "rs1654040870", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654040870" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804035", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P202", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.222.222", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654040658", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654040658", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654040658", "url": "https://www.ensembl.org/id/rs1654040658", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "NAFQYVQKNRGIDSEDAYPY", "down_seq": "GQEESCMYNPTGKAAKCRGY", "snv": [ { "evidence": [ { "id": "rs1654040658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654040658" }, { "id": "rs1654040658", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654040658" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804028", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V204", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.224.224", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "AFQYVQKNRGIDSEDAYPYV", "down_seq": "QEESCMYNPTGKAAKCRGYR", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804025", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G205", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.225.225", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs199555702", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199555702", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199555702", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199555702#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199555702", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199555702", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654040541", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654040541", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654040541", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654040541#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1654040541", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654040541", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "FQYVQKNRGIDSEDAYPYVG", "down_seq": "EESCMYNPTGKAAKCRGYRE", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs199555702", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199555702" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150804023", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q206", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs199555702", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199555702" }, { "id": "rs199555702", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199555702#frequency_tab" }, { "id": "rs199555702", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199555702" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804023", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q206", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs199555702", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199555702" }, { "id": "rs199555702", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199555702#frequency_tab" }, { "id": "rs199555702", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199555702" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804023", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q206", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654040541", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654040541" }, { "id": "rs1654040541", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654040541#frequency_tab" }, { "id": "rs1654040541", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654040541" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150804022", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q206", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1216299369", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216299369", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1216299369", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216299369", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs768562170", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768562170", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768562170", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768562170", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768562170", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768562170#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768562170", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768562170", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs777030210", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777030210", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777030210", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777030210", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777030210", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777030210#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777030210", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777030210", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "YVQKNRGIDSEDAYPYVGQE", "down_seq": "SCMYNPTGKAAKCRGYREIP", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799706", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E208", "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": "rs1216299369", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216299369" }, { "id": "rs1216299369", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216299369" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799705", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E208", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768562170", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768562170" }, { "id": "rs768562170", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768562170" }, { "id": "rs768562170", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768562170#frequency_tab" }, { "id": "rs768562170", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768562170" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799704", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E208", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs777030210", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777030210" }, { "id": "rs777030210", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777030210" }, { "id": "rs777030210", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777030210#frequency_tab" }, { "id": "rs777030210", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777030210" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799706", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E208", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs777030210", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777030210" }, { "id": "rs777030210", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777030210" }, { "id": "rs777030210", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777030210#frequency_tab" }, { "id": "rs777030210", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777030210" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799706", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E208", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.228.228", "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": 5 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "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": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs926584904", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs926584904", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs926584904", "url": "https://www.ncbi.nlm.nih.gov/snp/rs926584904#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs926584904", "url": "http://gnomad.broadinstitute.org/awesome?query=rs926584904", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1271585034", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1271585034", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1271585034", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1271585034#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1271585034", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1271585034", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1653949354", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653949354", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653949354", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653949354#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VQKNRGIDSEDAYPYVGQEE", "down_seq": "CMYNPTGKAAKCRGYREIPE", "snv": [ { "evidence": [ { "id": "rs926584904", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs926584904" }, { "id": "rs926584904", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs926584904#frequency_tab" }, { "id": "rs926584904", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs926584904" }, { "id": "rs1271585034", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1271585034" }, { "id": "rs1271585034", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1271585034#frequency_tab" }, { "id": "rs1271585034", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1271585034" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799703", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S209", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1653949354", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653949354" }, { "id": "rs1653949354", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653949354#frequency_tab" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799702", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S209", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.229.229", "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": 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": "P43235-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "QKNRGIDSEDAYPYVGQEES", "down_seq": "MYNPTGKAAKCRGYREIPEG", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799700", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "C210", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.230.230", "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": "P43235-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201800918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201800918", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201800918", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201800918", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201800918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201800918", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201800918", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201800918#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201800918", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201800918", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs780080857", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780080857", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780080857", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780080857", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780080857", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780080857", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "KNRGIDSEDAYPYVGQEESC", "down_seq": "YNPTGKAAKCRGYREIPEGN", "snv": [ { "evidence": [ { "id": "rs201800918", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201800918" }, { "id": "rs201800918", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201800918" }, { "id": "rs201800918", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201800918" }, { "id": "rs201800918", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201800918#frequency_tab" }, { "id": "rs201800918", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201800918" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799695", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "M211", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ] }, { "evidence": [ { "id": "rs780080857", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780080857" }, { "id": "rs780080857", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780080857" }, { "id": "rs780080857", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780080857" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799696", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M211", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.231.231", "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": 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": "P43235-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1202737189", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202737189", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1202737189", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1202737189", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NRGIDSEDAYPYVGQEESCM", "down_seq": "NPTGKAAKCRGYREIPEGNE", "snv": [ { "evidence": [ { "id": "rs1202737189", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202737189" }, { "id": "rs1202737189", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1202737189" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799693", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y212", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.232.232", "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": "P43235-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525166958", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166958", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RGIDSEDAYPYVGQEESCMY", "down_seq": "PTGKAAKCRGYREIPEGNEK", "snv": [ { "evidence": [ { "id": "rs2525166958", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166958" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799691_150799693", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N213", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.233.233", "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": 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": "P43235-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1557824710", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1557824710", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1557824710", "url": "https://www.ensembl.org/id/rs1557824710", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs778307801", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778307801", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778307801", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778307801", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778307801", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778307801", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DSEDAYPYVGQEESCMYNPT", "down_seq": "KAAKCRGYREIPEGNEKALK", "snv": [ { "evidence": [ { "id": "rs1557824710", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1557824710" }, { "id": "rs1557824710", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1557824710" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799682", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G216", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778307801", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778307801" }, { "id": "rs778307801", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778307801" }, { "id": "rs778307801", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778307801" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799681", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G216", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.234.234", "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": 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": "P43235-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1057516891", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516891", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SEDAYPYVGQEESCMYNPTG", "down_seq": "AAKCRGYREIPEGNEKALKR", "snv": [ { "evidence": [ { "id": "rs1057516891", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516891" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799680", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K217", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101948099", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101948099", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101948099", "url": "https://www.ensembl.org/id/rs2101948099", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2101948096", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101948096", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EDAYPYVGQEESCMYNPTGK", "down_seq": "AKCRGYREIPEGNEKALKRA", "snv": [ { "evidence": [ { "id": "rs2101948099", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101948099" }, { "id": "rs2101948099", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101948099" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799676", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A218", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101948096", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101948096" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799675", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A218", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.238.238", "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": "P43235-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525166892", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166892", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DAYPYVGQEESCMYNPTGKA", "down_seq": "KCRGYREIPEGNEKALKRAV", "snv": [ { "evidence": [ { "id": "rs2525166892", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166892" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799673", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A219", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.239.239", "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": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1231148306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1231148306", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1231148306", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1231148306", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "MWGLKVLLLPVVSFALYPEE", "down_seq": "LDTHWELWKKTHRKQYNNKV", "snv": [ { "evidence": [ { "id": "rs1231148306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1231148306" }, { "id": "rs1231148306", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1231148306" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806744", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I21", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.41.41", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1225660627", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225660627", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225660627", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1225660627#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AYPYVGQEESCMYNPTGKAA", "down_seq": "CRGYREIPEGNEKALKRAVA", "snv": [ { "evidence": [ { "id": "rs1225660627", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225660627" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799670", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K220", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1225660627", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225660627" }, { "id": "rs1225660627", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1225660627#frequency_tab" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799670", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K220", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.240.240", "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": 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": "P43235-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101948090", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101948090", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101948090", "url": "https://www.ensembl.org/id/rs2101948090", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "YPYVGQEESCMYNPTGKAAK", "down_seq": "RGYREIPEGNEKALKRAVAR", "snv": [ { "evidence": [ { "id": "rs2101948090", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101948090" }, { "id": "rs2101948090", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101948090" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799666", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C221", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.241.241", "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": "P43235-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1267654659", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1267654659", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1267654659", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1267654659#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1267654659", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1267654659", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PYVGQEESCMYNPTGKAAKC", "down_seq": "GYREIPEGNEKALKRAVARV", "snv": [ { "evidence": [ { "id": "rs1267654659", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1267654659" }, { "id": "rs1267654659", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1267654659#frequency_tab" }, { "id": "rs1267654659", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1267654659" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799664", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R222", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799663", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R222", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.242.242", "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": [ "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": "P43235-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763805411", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763805411", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763805411", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763805411", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763805411", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763805411", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1357652214", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357652214", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1357652214", "url": "https://www.ensembl.org/id/rs1357652214", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YVGQEESCMYNPTGKAAKCR", "down_seq": "YREIPEGNEKALKRAVARVG", "snv": [ { "evidence": [ { "id": "rs763805411", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763805411" }, { "id": "rs763805411", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763805411" }, { "id": "rs763805411", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763805411" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799660", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G223", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763805411", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763805411" }, { "id": "rs763805411", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763805411" }, { "id": "rs763805411", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763805411" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799660", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G223", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1357652214", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357652214" }, { "id": "rs1357652214", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1357652214" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799661", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G223", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.243.243", "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": 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": "P43235-1.224.224", "start_pos": 224, "end_pos": 224, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200236592", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200236592", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200236592", "url": "https://www.ensembl.org/id/rs200236592", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1202737189", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202737189", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1202737189", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1202737189", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200635611", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200635611", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200635611", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200635611", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200635611", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200635611", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200635611", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200635611", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1553196945", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553196945", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VGQEESCMYNPTGKAAKCRG", "down_seq": "REIPEGNEKALKRAVARVGP", "snv": [ { "evidence": [ { "id": "rs200236592", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200236592" }, { "id": "rs200236592", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs200236592" }, { "id": "rs1202737189", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202737189" }, { "id": "rs1202737189", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1202737189" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799657", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y224", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200635611", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200635611" }, { "id": "rs200635611", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200635611" }, { "id": "rs200635611", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200635611" }, { "id": "rs200635611", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200635611" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799658", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "Y224", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1553196945", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553196945" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799661", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y224", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.244.244", "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": 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": "P43235-1.225.225", "start_pos": 225, "end_pos": 225, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GQEESCMYNPTGKAAKCRGY", "down_seq": "EIPEGNEKALKRAVARVGPV", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799654", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R225", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.244.244", "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": "P43235-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs915360055", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs915360055", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs915360055", "url": "https://www.ncbi.nlm.nih.gov/snp/rs915360055#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs915360055", "url": "http://gnomad.broadinstitute.org/awesome?query=rs915360055", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QEESCMYNPTGKAAKCRGYR", "down_seq": "IPEGNEKALKRAVARVGPVS", "snv": [ { "evidence": [ { "id": "rs915360055", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs915360055" }, { "id": "rs915360055", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs915360055#frequency_tab" }, { "id": "rs915360055", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs915360055" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799651", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E226", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799652", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "E226", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.246.246", "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", "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": "P43235-1.227.227", "start_pos": 227, "end_pos": 227, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758450569", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758450569", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EESCMYNPTGKAAKCRGYRE", "down_seq": "PEGNEKALKRAVARVGPVSV", "snv": [ { "evidence": [ { "id": "rs758450569", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758450569" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799649_150799650in", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I227", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.246.246", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763405094", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763405094", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763405094", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763405094", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763405094", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763405094", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ESCMYNPTGKAAKCRGYREI", "down_seq": "EGNEKALKRAVARVGPVSVA", "snv": [ { "evidence": [ { "id": "rs763405094", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763405094" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799646", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P228", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763405094", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763405094" }, { "id": "rs763405094", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763405094" }, { "id": "rs763405094", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763405094" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799646", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P228", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.248.248", "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": 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": "P43235-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs200515162", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200515162", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200515162", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200515162", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200515162", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200515162#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200515162", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200515162", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SCMYNPTGKAAKCRGYREIP", "down_seq": "GNEKALKRAVARVGPVSVAI", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs200515162", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200515162" }, { "id": "rs200515162", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200515162" }, { "id": "rs200515162", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200515162#frequency_tab" }, { "id": "rs200515162", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200515162" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799643", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E229", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.249.249", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs145128083", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145128083", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145128083", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145128083", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145128083", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145128083#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145128083", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145128083", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs776595418", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776595418", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776595418", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776595418", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776595418", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776595418", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "WGLKVLLLPVVSFALYPEEI", "down_seq": "DTHWELWKKTHRKQYNNKVD", "snv": [ { "evidence": [ { "id": "rs145128083", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145128083" }, { "id": "rs145128083", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145128083" }, { "id": "rs145128083", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145128083#frequency_tab" }, { "id": "rs145128083", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145128083" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806742", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L22", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776595418", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776595418" }, { "id": "rs776595418", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776595418" }, { "id": "rs776595418", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776595418" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806741", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L22", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.42.42", "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": 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": "P43235-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs956544841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs956544841", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs956544841", "url": "https://www.ncbi.nlm.nih.gov/snp/rs956544841#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs956544841", "url": "http://gnomad.broadinstitute.org/awesome?query=rs956544841", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "CMYNPTGKAAKCRGYREIPE", "down_seq": "NEKALKRAVARVGPVSVAID", "snv": [ { "evidence": [ { "id": "rs956544841", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs956544841" }, { "id": "rs956544841", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs956544841#frequency_tab" }, { "id": "rs956544841", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs956544841" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799639", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G230", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.250.250", "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": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2525166561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166561", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MYNPTGKAAKCRGYREIPEG", "down_seq": "EKALKRAVARVGPVSVAIDA", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799637", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N231", "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": "rs2525166561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166561" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799641", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N231", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.250.250", "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": 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": "P43235-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "YNPTGKAAKCRGYREIPEGN", "down_seq": "KALKRAVARVGPVSVAIDAS", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150799632", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E232", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.252.252", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1653947344", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653947344", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653947344", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653947344#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PTGKAAKCRGYREIPEGNEK", "down_seq": "LKRAVARVGPVSVAIDASLT", "snv": [ { "evidence": [ { "id": "rs1653947344", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653947344" }, { "id": "rs1653947344", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653947344#frequency_tab" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799628", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A234", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1653947344", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653947344" }, { "id": "rs1653947344", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653947344#frequency_tab" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150799628", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A234", "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", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.254.254", "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": 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": "P43235-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs377253544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377253544", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377253544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377253544", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs377253544", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377253544#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs377253544", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377253544", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs202143753", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202143753", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202143753", "url": "https://www.ensembl.org/id/rs202143753", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KAAKCRGYREIPEGNEKALK", "down_seq": "AVARVGPVSVAIDASLTSFQ", "snv": [ { "evidence": [ { "id": "rs377253544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377253544" }, { "id": "rs377253544", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377253544" }, { "id": "rs377253544", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377253544#frequency_tab" }, { "id": "rs377253544", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377253544" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799618", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R237", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs202143753", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202143753" }, { "id": "rs202143753", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs202143753" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799617", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R237", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.255.255", "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": 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": "P43235-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525166522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166522", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AAKCRGYREIPEGNEKALKR", "down_seq": "VARVGPVSVAIDASLTSFQF", "snv": [ { "evidence": [ { "id": "rs2525166522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166522" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799616delinsATGCAAGCC", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A238", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.258.258", "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": 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": "P43235-1.239.239", "start_pos": 239, "end_pos": 239, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1385348098", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1385348098", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1385348098", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1385348098#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1385348098", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1385348098", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs776977098", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776977098", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776977098", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776977098", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776977098", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776977098", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "AKCRGYREIPEGNEKALKRA", "down_seq": "ARVGPVSVAIDASLTSFQFY", "snv": [ { "evidence": [ { "id": "rs1385348098", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1385348098" }, { "id": "rs1385348098", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1385348098#frequency_tab" }, { "id": "rs1385348098", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1385348098" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799612", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V239", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776977098", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776977098" }, { "id": "rs776977098", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776977098" }, { "id": "rs776977098", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776977098" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799613", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V239", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.259.259", "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": 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": "P43235-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769009784", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769009784", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769009784", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769009784", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769009784", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769009784#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769009784", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769009784", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KCRGYREIPEGNEKALKRAV", "down_seq": "RVGPVSVAIDASLTSFQFYS", "snv": [ { "evidence": [ { "id": "rs769009784", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769009784" }, { "id": "rs769009784", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769009784" }, { "id": "rs769009784", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769009784#frequency_tab" }, { "id": "rs769009784", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769009784" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799610", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A240", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs769009784", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769009784" }, { "id": "rs769009784", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769009784" }, { "id": "rs769009784", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769009784#frequency_tab" }, { "id": "rs769009784", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769009784" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799610", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A240", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.259.259", "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": 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": "P43235-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The gene for pycnodysostosis maps to human chromosome 1cen-q21.", "journal": "Nature genetics", "date": "1995-06", "authors": "Polymeropoulos M H, Ortiz De Luna R I, Ide S E, Torres R, Rubenstein J, Francomano C A", "evidence": [ { "database": "dbSNP", "id": "rs74315303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315303" } ], "reference": [ { "type": "PubMed", "id": "7663522", "url": "https://glygen.org/publication/PubMed/7663522" } ] }, { "title": "Pycnodysostosis, a lysosomal disease caused by cathepsin K deficiency.", "journal": "Science (New York, N.Y.)", "date": "1996", "authors": "Gelb BD, Shi GP, Chapman HA, Desnick RJ", "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" }, { "database": "dbSNP", "id": "rs74315302", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315302" }, { "database": "dbSNP", "id": "rs74315303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315303" } ], "reference": [ { "type": "PubMed", "id": "8703060", "url": "https://glygen.org/publication/PubMed/8703060" } ] }, { "title": "A nonsense mutation in the cathepsin K gene observed in a family with pycnodysostosis.", "journal": "Genome research", "date": "1996-11", "authors": "Johnson M R, Polymeropoulos M H, Vos H L, Ortiz de Luna R I, Francomano C A", "evidence": [ { "database": "dbSNP", "id": "rs74315303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315303" } ], "reference": [ { "type": "PubMed", "id": "8938428", "url": "https://glygen.org/publication/PubMed/8938428" } ] } ], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs74315303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315303", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs74315303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315303", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs74315303", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315303#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs74315303", "url": "http://gnomad.broadinstitute.org/awesome?query=rs74315303", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "7663522", "url": "https://glygen.org/publication/PubMed/7663522", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8703060", "url": "https://glygen.org/publication/PubMed/8703060", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8938428", "url": "https://glygen.org/publication/PubMed/8938428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs771997660", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771997660", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771997660", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771997660", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771997660", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771997660#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771997660", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771997660", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CRGYREIPEGNEKALKRAVA", "down_seq": "VGPVSVAIDASLTSFQFYSK", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs74315303", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315303" }, { "id": "rs74315303", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315303" }, { "id": "rs74315303", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315303#frequency_tab" }, { "id": "rs74315303", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs74315303" }, { "id": "7663522", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/7663522" }, { "id": "8703060", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8703060" }, { "id": "8938428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8938428" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799607", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R241", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs771997660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771997660" }, { "id": "rs771997660", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771997660" }, { "id": "rs771997660", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771997660#frequency_tab" }, { "id": "rs771997660", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771997660" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799606", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R241", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771997660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771997660" }, { "id": "rs771997660", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771997660" }, { "id": "rs771997660", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771997660#frequency_tab" }, { "id": "rs771997660", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771997660" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799606", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R241", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.261.261", "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": 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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43235-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745769874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745769874", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745769874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745769874", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745769874", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745769874", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2525166455", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166455", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "RGYREIPEGNEKALKRAVAR", "down_seq": "GPVSVAIDASLTSFQFYSKG", "snv": [ { "evidence": [ { "id": "rs745769874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745769874" }, { "id": "rs745769874", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745769874" }, { "id": "rs745769874", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745769874" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799604", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V242", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2525166455", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525166455" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799597_150799604", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V242", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.262.262", "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": 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": "P43235-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201851269", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201851269", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201851269", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201851269", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GYREIPEGNEKALKRAVARV", "down_seq": "PVSVAIDASLTSFQFYSKGV", "snv": [ { "evidence": [ { "id": "rs201851269", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201851269" }, { "id": "rs201851269", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201851269" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799601", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G243", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.263.263", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201022563", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201022563", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201022563", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201022563", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201022563", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201022563#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201022563", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201022563", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YREIPEGNEKALKRAVARVG", "down_seq": "VSVAIDASLTSFQFYSKGVY", "snv": [ { "evidence": [ { "id": "rs201022563", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201022563" }, { "id": "rs201022563", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201022563" }, { "id": "rs201022563", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201022563#frequency_tab" }, { "id": "rs201022563", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201022563" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799598", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P244", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.264.264", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs750699844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750699844", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIPEGNEKALKRAVARVGPV", "down_seq": "VAIDASLTSFQFYSKGVYYD", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799591", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S246", "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": "rs750699844", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750699844" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799591GA", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S246", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1335341275", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1335341275", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1335341275", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1335341275#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1335341275", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1335341275", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PEGNEKALKRAVARVGPVSV", "down_seq": "IDASLTSFQFYSKGVYYDES", "snv": [ { "evidence": [ { "id": "rs1335341275", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1335341275" }, { "id": "rs1335341275", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1335341275#frequency_tab" }, { "id": "rs1335341275", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1335341275" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799586", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A248", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799586", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A248", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs199919553", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199919553", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199919553", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199919553#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199919553", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199919553", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EGNEKALKRAVARVGPVSVA", "down_seq": "DASLTSFQFYSKGVYYDESC", "snv": [ { "evidence": [ { "id": "rs199919553", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199919553" }, { "id": "rs199919553", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199919553#frequency_tab" }, { "id": "rs199919553", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199919553" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799582", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I249", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs199919553", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199919553" }, { "id": "rs199919553", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199919553#frequency_tab" }, { "id": "rs199919553", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199919553" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799582", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I249", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 2 } ], "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": "P43235-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1294260185", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294260185", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1294260185", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1294260185#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LKVLLLPVVSFALYPEEILD", "down_seq": "HWELWKKTHRKQYNNKVDEI", "snv": [ { "evidence": [ { "id": "rs1294260185", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294260185" }, { "id": "rs1294260185", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1294260185#frequency_tab" } ], "glycoeffect": [], "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806735", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T24", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.253.253", "start_pos": 253, "end_pos": 253, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748857209", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748857209", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748857209", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748857209", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748857209", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748857209", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KALKRAVARVGPVSVAIDAS", "down_seq": "TSFQFYSKGVYYDESCNSDN", "snv": [ { "evidence": [ { "id": "rs748857209", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748857209" }, { "id": "rs748857209", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748857209" }, { "id": "rs748857209", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748857209" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799570", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L253", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.254.254", "start_pos": 254, "end_pos": 254, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1653945794", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653945794", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653945794", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653945794#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ALKRAVARVGPVSVAIDASL", "down_seq": "SFQFYSKGVYYDESCNSDNL", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150799567", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T254", "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": "rs1653945794", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653945794" }, { "id": "rs1653945794", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653945794#frequency_tab" } ], "glycoeffect": [], "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799568", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T254", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.274.274", "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": 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": "P43235-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKRAVARVGPVSVAIDASLT", "down_seq": "FQFYSKGVYYDESCNSDNLN", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150799564", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S255", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.274.274", "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": "P43235-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "AVARVGPVSVAIDASLTSFQ", "down_seq": "YSKGVYYDESCNSDNLNHAV", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799556", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "F258", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.278.278", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.259.259", "start_pos": 259, "end_pos": 259, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1653945620", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653945620", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653945620", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653945620#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1653945620", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653945620", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1250833583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250833583", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1250833583", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250833583", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VARVGPVSVAIDASLTSFQF", "down_seq": "SKGVYYDESCNSDNLNHAVL", "snv": [ { "evidence": [ { "id": "rs1653945620", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653945620" }, { "id": "rs1653945620", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653945620#frequency_tab" }, { "id": "rs1653945620", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653945620" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799552", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y259", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1250833583", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250833583" }, { "id": "rs1250833583", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250833583" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799553", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y259", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.278.278", "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": "P43235-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1371698411", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1371698411", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1371698411", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1371698411", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "KVLLLPVVSFALYPEEILDT", "down_seq": "WELWKKTHRKQYNNKVDEIS", "snv": [ { "evidence": [ { "id": "rs1371698411", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1371698411" }, { "id": "rs1371698411", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1371698411" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806733", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H25", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101947967", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947967", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101947967", "url": "https://www.ensembl.org/id/rs2101947967", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RVGPVSVAIDASLTSFQFYS", "down_seq": "GVYYDESCNSDNLNHAVLAV", "snv": [ { "evidence": [ { "id": "rs2101947967", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947967" }, { "id": "rs2101947967", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101947967" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799546", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K261", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VGPVSVAIDASLTSFQFYSK", "down_seq": "VYYDESCNSDNLNHAVLAVG", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799544", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G262", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1653936233", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653936233", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653936233", "url": "https://www.ensembl.org/id/rs1653936233", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "GPVSVAIDASLTSFQFYSKG", "down_seq": "YYDESCNSDNLNHAVLAVGY", "snv": [ { "evidence": [ { "id": "rs1653936233", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653936233" }, { "id": "rs1653936233", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1653936233" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799270", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V263", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.283.283", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1653936192", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653936192", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653936192", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653936192#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PVSVAIDASLTSFQFYSKGV", "down_seq": "YDESCNSDNLNHAVLAVGYG", "snv": [ { "evidence": [ { "id": "rs1653936192", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653936192" }, { "id": "rs1653936192", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653936192#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799267", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y264", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101947712", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947712", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101947712", "url": "https://www.ensembl.org/id/rs2101947712", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VSVAIDASLTSFQFYSKGVY", "down_seq": "DESCNSDNLNHAVLAVGYGI", "snv": [ { "evidence": [ { "id": "rs2101947712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947712" }, { "id": "rs2101947712", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101947712" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799264", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y265", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525180527", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180527", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "VLLLPVVSFALYPEEILDTH", "down_seq": "ELWKKTHRKQYNNKVDEISR", "snv": [ { "evidence": [ { "id": "rs2525180527", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180527" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806728", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W26", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "W", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806729", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "W26", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.46.46", "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", "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": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1182949377", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1182949377", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1182949377", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1182949377", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2101947699", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947699", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101947699", "url": "https://www.ensembl.org/id/rs2101947699", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DASLTSFQFYSKGVYYDESC", "down_seq": "SDNLNHAVLAVGYGIQKGNK", "snv": [ { "evidence": [ { "id": "rs1182949377", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1182949377" }, { "id": "rs1182949377", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1182949377" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799250", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N270", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101947699", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947699" }, { "id": "rs2101947699", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101947699" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799249", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N270", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.290.290", "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": "P43235-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1160880587", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1160880587", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1160880587", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1160880587", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs183135762", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs183135762", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs183135762", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs183135762", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs183135762", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs183135762", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs183135762", "url": "https://www.ncbi.nlm.nih.gov/snp/rs183135762#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs183135762", "url": "http://gnomad.broadinstitute.org/awesome?query=rs183135762", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASLTSFQFYSKGVYYDESCN", "down_seq": "DNLNHAVLAVGYGIQKGNKH", "snv": [ { "evidence": [ { "id": "rs1160880587", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1160880587" }, { "id": "rs1160880587", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1160880587" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799247", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S271", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799247", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S271", "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": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799246", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S271", "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": "rs183135762", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs183135762" }, { "id": "rs183135762", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs183135762" }, { "id": "rs183135762", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs183135762" }, { "id": "rs183135762", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs183135762#frequency_tab" }, { "id": "rs183135762", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs183135762" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799246", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S271", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 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_non_disease", "table_stats": [ { "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": "P43235-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs190892496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190892496", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs190892496", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190892496", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs190892496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190892496", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs190892496", "url": "https://www.ncbi.nlm.nih.gov/snp/rs190892496#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs190892496", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190892496", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201772791", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201772791", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201772791", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201772791", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201772791", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201772791#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201772791", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201772791", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SLTSFQFYSKGVYYDESCNS", "down_seq": "NLNHAVLAVGYGIQKGNKHW", "snv": [ { "evidence": [ { "id": "rs190892496", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190892496" }, { "id": "rs190892496", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190892496" }, { "id": "rs190892496", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190892496" }, { "id": "rs190892496", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs190892496#frequency_tab" }, { "id": "rs190892496", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190892496" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799242", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "D272", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs201772791", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201772791" }, { "id": "rs201772791", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201772791" }, { "id": "rs201772791", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201772791#frequency_tab" }, { "id": "rs201772791", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201772791" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799244", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D272", "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" } ] }, { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779217918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779217918", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779217918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779217918", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779217918", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779217918#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779217918", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779217918", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1653935181", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653935181", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LTSFQFYSKGVYYDESCNSD", "down_seq": "LNHAVLAVGYGIQKGNKHWI", "snv": [ { "evidence": [ { "id": "rs779217918", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779217918" }, { "id": "rs779217918", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779217918" }, { "id": "rs779217918", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779217918#frequency_tab" }, { "id": "rs779217918", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779217918" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799241", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N273", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779217918", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779217918" }, { "id": "rs779217918", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779217918" }, { "id": "rs779217918", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779217918#frequency_tab" }, { "id": "rs779217918", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779217918" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799241", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N273", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1653935181", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653935181" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799241", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N273", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.293.293", "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": "P43235-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "TSFQFYSKGVYYDESCNSDN", "down_seq": "NHAVLAVGYGIQKGNKHWII", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799237", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L274", "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": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799238", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L274", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.293.293", "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": 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": "P43235-1.276.276", "start_pos": 276, "end_pos": 276, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101947647", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947647", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101947647", "url": "https://www.ensembl.org/id/rs2101947647", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1571123333", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571123333", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571123333", "url": "https://www.ensembl.org/id/rs1571123333", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1553196906", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553196906", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "FQFYSKGVYYDESCNSDNLN", "down_seq": "AVLAVGYGIQKGNKHWIIKN", "snv": [ { "evidence": [ { "id": "rs2101947647", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947647" }, { "id": "rs2101947647", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101947647" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799231", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H276", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1571123333", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571123333" }, { "id": "rs1571123333", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1571123333" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799232", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H276", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1553196906", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553196906" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799233", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H276", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 3 } ], "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": "P43235-1.277.277", "start_pos": 277, "end_pos": 277, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Paternal uniparental disomy for chromosome 1 revealed by molecular analysis of a patient with pycnodysostosis.", "journal": "American journal of human genetics", "date": "1998", "authors": "Gelb BD, Willner JP, Dunn TM, Kardon NB, Verloes A, Poncin J, Desnick RJ", "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" }, { "database": "dbSNP", "id": "rs74315304", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315304" } ], "reference": [ { "type": "PubMed", "id": "9529353", "url": "https://glygen.org/publication/PubMed/9529353" } ] } ], "crossref": [ { "id": "rs74315304", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315304", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs74315304", "url": "http://gnomad.broadinstitute.org/awesome?query=rs74315304", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "9529353", "url": "https://glygen.org/publication/PubMed/9529353", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QFYSKGVYYDESCNSDNLNH", "down_seq": "VLAVGYGIQKGNKHWIIKNS", "snv": [ { "evidence": [ { "id": "rs74315304", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315304" }, { "id": "rs74315304", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs74315304" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799228", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A277", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs74315304", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315304" }, { "id": "rs74315304", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs74315304" }, { "id": "9529353", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9529353" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150799228", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A277", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43235-1.278.278", "start_pos": 278, "end_pos": 278, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1571123285", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571123285", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571123285", "url": "https://www.ensembl.org/id/rs1571123285", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1463682255", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463682255", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1463682255", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463682255", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "FYSKGVYYDESCNSDNLNHA", "down_seq": "LAVGYGIQKGNKHWIIKNSW", "snv": [ { "evidence": [ { "id": "rs1571123285", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571123285" }, { "id": "rs1571123285", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1571123285" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799225", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V278", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799225", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "V278", "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": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1463682255", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463682255" }, { "id": "rs1463682255", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463682255" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799226", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V278", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.298.298", "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", "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": "P43235-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746596138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746596138", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746596138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746596138", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746596138", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746596138#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746596138", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746596138", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LLLPVVSFALYPEEILDTHW", "down_seq": "LWKKTHRKQYNNKVDEISRR", "snv": [ { "evidence": [ { "id": "rs746596138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746596138" }, { "id": "rs746596138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746596138" }, { "id": "rs746596138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746596138#frequency_tab" }, { "id": "rs746596138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746596138" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806727", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E27", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746596138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746596138" }, { "id": "rs746596138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746596138" }, { "id": "rs746596138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746596138#frequency_tab" }, { "id": "rs746596138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746596138" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806727", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E27", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.47.47", "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": 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": "P43235-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1653934092", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653934092", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653934092", "url": "https://www.ensembl.org/id/rs1653934092", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SKGVYYDESCNSDNLNHAVL", "down_seq": "VGYGIQKGNKHWIIKNSWGE", "snv": [ { "evidence": [ { "id": "rs1653934092", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653934092" }, { "id": "rs1653934092", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1653934092" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799219", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A280", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525165528", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525165528", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VYYDESCNSDNLNHAVLAVG", "down_seq": "GIQKGNKHWIIKNSWGENWG", "snv": [ { "evidence": [ { "id": "rs2525165528", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525165528" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799211", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y283", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799211", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y283", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.284.284", "start_pos": 284, "end_pos": 284, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YYDESCNSDNLNHAVLAVGY", "down_seq": "IQKGNKHWIIKNSWGENWGN", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150799207", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G284", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1229188322", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229188322", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1229188322", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1229188322", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "DESCNSDNLNHAVLAVGYGI", "down_seq": "KGNKHWIIKNSWGENWGNKG", "snv": [ { "evidence": [ { "id": "rs1229188322", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229188322" }, { "id": "rs1229188322", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1229188322" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799201", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q286", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.288.288", "start_pos": 288, "end_pos": 288, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1653933557", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653933557", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653933557", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653933557#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SCNSDNLNHAVLAVGYGIQK", "down_seq": "NKHWIIKNSWGENWGNKGYI", "snv": [ { "evidence": [ { "id": "rs1653933557", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653933557" }, { "id": "rs1653933557", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653933557#frequency_tab" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799195", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G288", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150799196", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G288", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774989958", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774989958", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774989958", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774989958", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774989958", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774989958#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774989958", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774989958", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LLPVVSFALYPEEILDTHWE", "down_seq": "WKKTHRKQYNNKVDEISRRL", "snv": [ { "evidence": [ { "id": "rs774989958", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774989958" }, { "id": "rs774989958", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774989958" }, { "id": "rs774989958", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774989958#frequency_tab" }, { "id": "rs774989958", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774989958" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806724", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L28", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.47.47", "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": "P43235-1.290.290", "start_pos": 290, "end_pos": 290, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752859354", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752859354", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752859354", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752859354", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752859354", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752859354", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NSDNLNHAVLAVGYGIQKGN", "down_seq": "HWIIKNSWGENWGNKGYILM", "snv": [ { "evidence": [ { "id": "rs752859354", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752859354" }, { "id": "rs752859354", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752859354" }, { "id": "rs752859354", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752859354" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799189", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K290", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.291.291", "start_pos": 291, "end_pos": 291, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1653933311", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653933311", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653933311", "url": "https://www.ensembl.org/id/rs1653933311", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SDNLNHAVLAVGYGIQKGNK", "down_seq": "WIIKNSWGENWGNKGYILMA", "snv": [ { "evidence": [ { "id": "rs1653933311", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653933311" }, { "id": "rs1653933311", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1653933311" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799187", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H291", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1553196900", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553196900", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1553196900", "url": "https://www.ensembl.org/id/rs1553196900", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "DNLNHAVLAVGYGIQKGNKH", "down_seq": "IIKNSWGENWGNKGYILMAR", "snv": [ { "evidence": [ { "id": "rs1553196900", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553196900" }, { "id": "rs1553196900", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1553196900" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799182", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W292", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.293.293", "start_pos": 293, "end_pos": 293, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767837525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767837525", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767837525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767837525", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767837525", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767837525", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1365258954", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365258954", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1365258954", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1365258954#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1365258954", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1365258954", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "NLNHAVLAVGYGIQKGNKHW", "down_seq": "IKNSWGENWGNKGYILMARN", "snv": [ { "evidence": [ { "id": "rs767837525", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767837525" }, { "id": "rs767837525", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767837525" }, { "id": "rs767837525", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767837525" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799179", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I293", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1365258954", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365258954" }, { "id": "rs1365258954", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1365258954#frequency_tab" }, { "id": "rs1365258954", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1365258954" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799180", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I293", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.313.313", "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": 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": "P43235-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101947591", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947591", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101947591", "url": "https://www.ensembl.org/id/rs2101947591", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NHAVLAVGYGIQKGNKHWII", "down_seq": "NSWGENWGNKGYILMARNKN", "snv": [ { "evidence": [ { "id": "rs2101947591", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101947591" }, { "id": "rs2101947591", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101947591" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150799174", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K295", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757744218", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757744218", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757744218", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757744218", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757744218", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757744218", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1237746431", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237746431", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1237746431", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1237746431#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1237746431", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237746431", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "VLAVGYGIQKGNKHWIIKNS", "down_seq": "GENWGNKGYILMARNKNNAC", "snv": [ { "evidence": [ { "id": "rs757744218", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757744218" }, { "id": "rs757744218", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757744218" }, { "id": "rs757744218", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757744218" }, { "id": "rs1237746431", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237746431" }, { "id": "rs1237746431", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1237746431#frequency_tab" }, { "id": "rs1237746431", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237746431" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796896", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W298", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.318.318", "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": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.299.299", "start_pos": 299, "end_pos": 299, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1438081443", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438081443", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1438081443", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1438081443#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1438081443", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438081443", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LAVGYGIQKGNKHWIIKNSW", "down_seq": "ENWGNKGYILMARNKNNACG", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796894", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G299", "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": "rs1438081443", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438081443" }, { "id": "rs1438081443", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1438081443#frequency_tab" }, { "id": "rs1438081443", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438081443" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796893", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G299", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796893", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G299", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1654099146", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654099146", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654099146", "url": "https://www.ensembl.org/id/rs1654099146", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2101954034", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101954034", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "LPVVSFALYPEEILDTHWEL", "down_seq": "KKTHRKQYNNKVDEISRRLI", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1654099146", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654099146" }, { "id": "rs1654099146", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654099146" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806719", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W29", "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": "rs2101954034", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101954034" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806723", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W29", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.49.49", "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": 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": "P43235-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654102585", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654102585", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654102585", "url": "https://www.ensembl.org/id/rs1654102585", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "M", "down_seq": "GLKVLLLPVVSFALYPEEIL", "snv": [ { "evidence": [ { "id": "rs1654102585", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654102585" }, { "id": "rs1654102585", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654102585" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806801", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W2", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 1, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AVGYGIQKGNKHWIIKNSWG", "down_seq": "NWGNKGYILMARNKNNACGI", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796891", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E300", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778490830", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778490830", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778490830", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778490830#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778490830", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778490830", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VGYGIQKGNKHWIIKNSWGE", "down_seq": "WGNKGYILMARNKNNACGIA", "snv": [ { "evidence": [ { "id": "rs778490830", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830" }, { "id": "rs778490830", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830" }, { "id": "rs778490830", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778490830#frequency_tab" }, { "id": "rs778490830", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778490830" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796888", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N301", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796888", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N301", "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": "rs778490830", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830" }, { "id": "rs778490830", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830" }, { "id": "rs778490830", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778490830#frequency_tab" }, { "id": "rs778490830", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778490830" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796888", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N301", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1237746431", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237746431", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1237746431", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1237746431#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1237746431", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237746431", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs757744218", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757744218", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757744218", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757744218", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757744218", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757744218", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1571122183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571122183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571122183", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1571122183#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1571122183", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1571122183", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "GYGIQKGNKHWIIKNSWGEN", "down_seq": "GNKGYILMARNKNNACGIAN", "snv": [ { "evidence": [ { "id": "rs1237746431", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237746431" }, { "id": "rs1237746431", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1237746431#frequency_tab" }, { "id": "rs1237746431", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237746431" }, { "id": "rs757744218", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757744218" }, { "id": "rs757744218", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757744218" }, { "id": "rs757744218", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757744218" }, { "id": "rs1571122183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571122183" }, { "id": "rs1571122183", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1571122183#frequency_tab" }, { "id": "rs1571122183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1571122183" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796895", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W302", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.303.303", "start_pos": 303, "end_pos": 303, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1438081443", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438081443", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1438081443", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1438081443#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1438081443", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438081443", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs756250449", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756250449", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756250449", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756250449", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756250449", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756250449#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756250449", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756250449", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2101946013", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101946013", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101946013", "url": "https://www.ensembl.org/id/rs2101946013", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2525161997", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525161997", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YGIQKGNKHWIIKNSWGENW", "down_seq": "NKGYILMARNKNNACGIANL", "snv": [ { "evidence": [ { "id": "rs1438081443", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438081443" }, { "id": "rs1438081443", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1438081443#frequency_tab" }, { "id": "rs1438081443", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438081443" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796893", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G303", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs756250449", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756250449" }, { "id": "rs756250449", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756250449" }, { "id": "rs756250449", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756250449#frequency_tab" }, { "id": "rs756250449", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756250449" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796881", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G303", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101946013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101946013" }, { "id": "rs2101946013", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101946013" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796882", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G303", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2525161997", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525161997" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796884", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G303", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "QKGNKHWIIKNSWGENWGNK", "down_seq": "YILMARNKNNACGIANLASF", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796872", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G306", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1418941229", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1418941229", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1418941229", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1418941229", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KGNKHWIIKNSWGENWGNKG", "down_seq": "ILMARNKNNACGIANLASFP", "snv": [ { "evidence": [ { "id": "rs1418941229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1418941229" }, { "id": "rs1418941229", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1418941229" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796868", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y307", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1433096776", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1433096776", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1433096776", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1433096776#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1653885698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653885698", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653885698", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653885698", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "GNKHWIIKNSWGENWGNKGY", "down_seq": "LMARNKNNACGIANLASFPK", "snv": [ { "evidence": [ { "id": "rs1433096776", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1433096776" }, { "id": "rs1433096776", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1433096776#frequency_tab" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796866", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I308", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1653885698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653885698" }, { "id": "rs1653885698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653885698" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796867", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I308", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.309.309", "start_pos": 309, "end_pos": 309, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cathepsin K gene mutations and 1q21 haplotypes in at patients with pycnodysostosis in an outbred population.", "journal": "European journal of human genetics : EJHG", "date": "2000", "authors": "Haagerup A, Hertz JM, Christensen MF, Binderup H, Kruse TA", "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" }, { "database": "dbSNP", "id": "rs29001685", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs29001685" } ], "reference": [ { "type": "PubMed", "id": "10878663", "url": "https://glygen.org/publication/PubMed/10878663" } ] } ], "crossref": [ { "id": "rs587638055", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587638055", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs587638055", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587638055", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs587638055", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587638055", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs587638055", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587638055", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs29001685", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs29001685", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs29001685", "url": "https://www.ncbi.nlm.nih.gov/snp/rs29001685#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs29001685", "url": "http://gnomad.broadinstitute.org/awesome?query=rs29001685", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "10878663", "url": "https://glygen.org/publication/PubMed/10878663", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NKHWIIKNSWGENWGNKGYI", "down_seq": "MARNKNNACGIANLASFPKM", "snv": [ { "evidence": [ { "id": "rs587638055", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587638055" }, { "id": "rs587638055", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587638055" }, { "id": "rs587638055", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587638055" }, { "id": "rs587638055", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587638055" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796864", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "L309", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs29001685", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs29001685" }, { "id": "rs29001685", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs29001685#frequency_tab" }, { "id": "rs29001685", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs29001685" }, { "id": "10878663", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/10878663" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796863", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L309", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43235-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1456718820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456718820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1456718820", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456718820#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1456718820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456718820", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PVVSFALYPEEILDTHWELW", "down_seq": "KTHRKQYNNKVDEISRRLIW", "snv": [ { "evidence": [ { "id": "rs1456718820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456718820" }, { "id": "rs1456718820", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456718820#frequency_tab" }, { "id": "rs1456718820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456718820" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806717", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K30", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.50.50", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1245231987", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245231987", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1245231987", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1245231987", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1653885392", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653885392", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653885392", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653885392#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1653885392", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653885392", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HWIIKNSWGENWGNKGYILM", "down_seq": "RNKNNACGIANLASFPKM", "snv": [ { "evidence": [ { "id": "rs1245231987", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245231987" }, { "id": "rs1245231987", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1245231987" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796858", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A311", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1653885392", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653885392" }, { "id": "rs1653885392", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653885392#frequency_tab" }, { "id": "rs1653885392", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653885392" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796857", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A311", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs375958814", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375958814", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375958814", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375958814", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs375958814", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375958814#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs375958814", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375958814", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1653885221", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653885221", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653885221", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653885221", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WIIKNSWGENWGNKGYILMA", "down_seq": "NKNNACGIANLASFPKM", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs375958814", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375958814" }, { "id": "rs375958814", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375958814" }, { "id": "rs375958814", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375958814#frequency_tab" }, { "id": "rs375958814", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375958814" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796855", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R312", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs375958814", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375958814" }, { "id": "rs375958814", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375958814" }, { "id": "rs375958814", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375958814#frequency_tab" }, { "id": "rs375958814", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375958814" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796855", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R312", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1653885221", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653885221" }, { "id": "rs1653885221", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653885221" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796854", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R312", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778490830", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778490830", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778490830", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778490830#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778490830", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778490830", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs199882930", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199882930", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199882930", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199882930#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199882930", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199882930", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IIKNSWGENWGNKGYILMAR", "down_seq": "KNNACGIANLASFPKM", "snv": [ { "evidence": [ { "id": "rs778490830", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830" }, { "id": "rs778490830", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830" }, { "id": "rs778490830", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778490830#frequency_tab" }, { "id": "rs778490830", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778490830" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796888", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N313", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs199882930", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199882930" }, { "id": "rs199882930", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199882930#frequency_tab" }, { "id": "rs199882930", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199882930" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796851", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N313", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778490830", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830" }, { "id": "rs778490830", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778490830" }, { "id": "rs778490830", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778490830#frequency_tab" }, { "id": "rs778490830", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778490830" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796888", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N313", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201702611", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201702611", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201702611", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201702611", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201702611", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201702611", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IKNSWGENWGNKGYILMARN", "down_seq": "NNACGIANLASFPKM", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150796847", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K314", "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": "rs201702611", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201702611" }, { "id": "rs201702611", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201702611" }, { "id": "rs201702611", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201702611" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796849", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K314", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.316.316", "start_pos": 316, "end_pos": 316, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101945969", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101945969", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101945969", "url": "https://www.ensembl.org/id/rs2101945969", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2525161846", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525161846", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NSWGENWGNKGYILMARNKN", "down_seq": "ACGIANLASFPKM", "snv": [ { "evidence": [ { "id": "rs2101945969", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101945969" }, { "id": "rs2101945969", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101945969" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796843", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N316", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2525161846", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525161846" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796841_150796842", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N316", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.318.318", "start_pos": 318, "end_pos": 318, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs762780994", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762780994", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762780994", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762780994", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762780994", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762780994#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762780994", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762780994", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "WGENWGNKGYILMARNKNNA", "down_seq": "GIANLASFPKM", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150796836", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "C318", "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": "rs762780994", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762780994" }, { "id": "rs762780994", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762780994" }, { "id": "rs762780994", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762780994#frequency_tab" }, { "id": "rs762780994", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762780994" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796836", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C318", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773116784", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773116784", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773116784", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773116784", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773116784", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773116784", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GENWGNKGYILMARNKNNAC", "down_seq": "IANLASFPKM", "snv": [ { "evidence": [ { "id": "rs773116784", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773116784" }, { "id": "rs773116784", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773116784" }, { "id": "rs773116784", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773116784" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796834", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G319", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.329.329", "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": "P43235-1.31.31", "start_pos": 31, "end_pos": 31, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654098990", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654098990", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654098990", "url": "https://www.ensembl.org/id/rs1654098990", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VVSFALYPEEILDTHWELWK", "down_seq": "THRKQYNNKVDEISRRLIWE", "snv": [ { "evidence": [ { "id": "rs1654098990", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654098990" }, { "id": "rs1654098990", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654098990" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806714", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K31", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 17, "direction": "downstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.51.51", "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": "P43235-1.320.320", "start_pos": 320, "end_pos": 320, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1433096776", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1433096776", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1433096776", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1433096776#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1653884612", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653884612", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653884612", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653884612#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1653885698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653885698", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653885698", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653885698", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "ENWGNKGYILMARNKNNACG", "down_seq": "ANLASFPKM", "snv": [ { "evidence": [ { "id": "rs1433096776", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1433096776" }, { "id": "rs1433096776", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1433096776#frequency_tab" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796866", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I320", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1653884612", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653884612" }, { "id": "rs1653884612", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653884612#frequency_tab" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796830", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I320", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1653885698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653885698" }, { "id": "rs1653885698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1653885698" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796867", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I320", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1653884829", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653884829", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1653884829", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653884829#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs587756638", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587756638", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs587756638", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587756638", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs587756638", "url": "https://www.ncbi.nlm.nih.gov/snp/rs587756638#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs587756638", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587756638", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NWGNKGYILMARNKNNACGI", "down_seq": "NLASFPKM", "snv": [ { "evidence": [ { "id": "rs1653884829", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653884829" }, { "id": "rs1653884829", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653884829#frequency_tab" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796839", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A321", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs587756638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587756638" }, { "id": "rs587756638", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587756638" }, { "id": "rs587756638", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs587756638#frequency_tab" }, { "id": "rs587756638", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587756638" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796840", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A321", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1653884829", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1653884829" }, { "id": "rs1653884829", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1653884829#frequency_tab" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796839", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A321", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.322.322", "start_pos": 322, "end_pos": 322, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1571122109", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571122109", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571122109", "url": "https://www.ensembl.org/id/rs1571122109", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "WGNKGYILMARNKNNACGIA", "down_seq": "LASFPKM", "snv": [ { "evidence": [ { "id": "rs1571122109", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571122109" }, { "id": "rs1571122109", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1571122109" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796824", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N322", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.329.329", "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": "P43235-1.326.326", "start_pos": 326, "end_pos": 326, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101945936", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101945936", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101945936", "url": "https://www.ensembl.org/id/rs2101945936", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "GYILMARNKNNACGIANLAS", "down_seq": "PKM", "snv": [ { "evidence": [ { "id": "rs2101945936", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101945936" }, { "id": "rs2101945936", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101945936" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796813", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F326", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.329.329", "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": "P43235-1.328.328", "start_pos": 328, "end_pos": 328, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752348151", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752348151", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752348151", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752348151#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752348151", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752348151", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200118513", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200118513", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200118513", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200118513#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200118513", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200118513", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ILMARNKNNACGIANLASFP", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs752348151", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752348151" }, { "id": "rs752348151", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752348151#frequency_tab" }, { "id": "rs752348151", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752348151" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796805", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K328", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200118513", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200118513" }, { "id": "rs200118513", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200118513#frequency_tab" }, { "id": "rs200118513", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200118513" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796806", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K328", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200118513", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200118513" }, { "id": "rs200118513", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200118513#frequency_tab" }, { "id": "rs200118513", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200118513" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796806", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K328", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.329.329", "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": 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": "P43235-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761159349", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761159349", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761159349", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761159349", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761159349", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761159349", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201817083", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201817083", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201817083", "url": "https://www.ensembl.org/id/rs201817083", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "LMARNKNNACGIANLASFPK", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs761159349", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761159349" }, { "id": "rs761159349", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761159349" }, { "id": "rs761159349", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761159349" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796802", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M329", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201817083", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201817083" }, { "id": "rs201817083", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs201817083" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150796804", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M329", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.316.316", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.322.322", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.328.328", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs267598007", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267598007", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs267598007", "url": "https://www.ensembl.org/id/rs267598007", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SFALYPEEILDTHWELWKKT", "down_seq": "RKQYNNKVDEISRRLIWEKN", "snv": [ { "evidence": [ { "id": "rs267598007", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267598007" }, { "id": "rs267598007", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs267598007" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806709", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H33", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.53.53", "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": "P43235-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654098874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654098874", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654098874", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654098874#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FALYPEEILDTHWELWKKTH", "down_seq": "KQYNNKVDEISRRLIWEKNL", "snv": [ { "evidence": [ { "id": "rs1654098874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654098874" }, { "id": "rs1654098874", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654098874#frequency_tab" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806706", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R34", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.53.53", "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": "P43235-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1395384909", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395384909", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1395384909", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1395384909", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs763148656", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763148656", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ALYPEEILDTHWELWKKTHR", "down_seq": "QYNNKVDEISRRLIWEKNLK", "snv": [ { "evidence": [ { "id": "rs1395384909", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395384909" }, { "id": "rs1395384909", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1395384909" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806701", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K35", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763148656", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763148656" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806702_150806704", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K35", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.55.55", "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": 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": "P43235-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1460106966", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1460106966", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1460106966", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1460106966", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LYPEEILDTHWELWKKTHRK", "down_seq": "YNNKVDEISRRLIWEKNLKY", "snv": [ { "evidence": [ { "id": "rs1460106966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1460106966" }, { "id": "rs1460106966", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1460106966" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806698", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q36", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.56.56", "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": "P43235-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs878961164", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs878961164", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs878961164", "url": "http://gnomad.broadinstitute.org/awesome?query=rs878961164", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YPEEILDTHWELWKKTHRKQ", "down_seq": "NNKVDEISRRLIWEKNLKYI", "snv": [ { "evidence": [ { "id": "rs878961164", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs878961164" }, { "id": "rs878961164", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs878961164" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806696", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y37", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.57.57", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654098496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654098496", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654098496", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654098496#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2525180438", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180438", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PEEILDTHWELWKKTHRKQY", "down_seq": "NKVDEISRRLIWEKNLKYIS", "snv": [ { "evidence": [ { "id": "rs1654098496", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654098496" }, { "id": "rs1654098496", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654098496#frequency_tab" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806692", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N38", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2525180438", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180438" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806694", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N38", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.58.58", "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" ] }, { "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": "P43235-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs369459638", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369459638", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369459638", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369459638", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369459638", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369459638#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369459638", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369459638", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs771768736", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771768736", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771768736", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771768736", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771768736", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771768736#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771768736", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771768736", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750595350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750595350", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EEILDTHWELWKKTHRKQYN", "down_seq": "KVDEISRRLIWEKNLKYISI", "snv": [ { "evidence": [ { "id": "rs369459638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369459638" }, { "id": "rs369459638", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369459638" }, { "id": "rs369459638", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369459638#frequency_tab" }, { "id": "rs369459638", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369459638" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806689", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N39", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771768736", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771768736" }, { "id": "rs771768736", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771768736" }, { "id": "rs771768736", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771768736#frequency_tab" }, { "id": "rs771768736", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771768736" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806691", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N39", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs750595350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750595350" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806689GTT", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N39", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.58.58", "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" ] }, { "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" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs202055627", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202055627", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202055627", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202055627", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs202055627", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202055627", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs202055627", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202055627#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs202055627", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202055627", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs756695909", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756695909", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756695909", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756695909", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756695909", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756695909", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MW", "down_seq": "LKVLLLPVVSFALYPEEILD", "snv": [ { "evidence": [ { "id": "rs202055627", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202055627" }, { "id": "rs202055627", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202055627" }, { "id": "rs202055627", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202055627" }, { "id": "rs202055627", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202055627#frequency_tab" }, { "id": "rs202055627", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202055627" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806798", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G3", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs756695909", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756695909" }, { "id": "rs756695909", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756695909" }, { "id": "rs756695909", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756695909" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806799", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G3", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 2, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101953982", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953982", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953982", "url": "https://www.ensembl.org/id/rs2101953982", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2525180406", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180406", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EILDTHWELWKKTHRKQYNN", "down_seq": "VDEISRRLIWEKNLKYISIH", "snv": [ { "evidence": [ { "id": "rs2101953982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953982" }, { "id": "rs2101953982", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953982" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806688", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K40", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2525180406", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180406" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806688", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K40", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.60.60", "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": 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": "P43235-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654090957", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654090957", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654090957", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654090957", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ILDTHWELWKKTHRKQYNNK", "down_seq": "DEISRRLIWEKNLKYISIHN", "snv": [ { "evidence": [ { "id": "rs1654090957", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654090957" }, { "id": "rs1654090957", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654090957" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806224", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V41", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654090957", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654090957" }, { "id": "rs1654090957", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654090957" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806224", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V41", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.60.60", "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": 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": "P43235-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1455123959", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1455123959", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1455123959", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1455123959", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LDTHWELWKKTHRKQYNNKV", "down_seq": "EISRRLIWEKNLKYISIHNL", "snv": [ { "evidence": [ { "id": "rs1455123959", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1455123959" }, { "id": "rs1455123959", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1455123959" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806221", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D42", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1455123959", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1455123959" }, { "id": "rs1455123959", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1455123959" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806221", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D42", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.62.62", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "P43235-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525178878", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178878", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DTHWELWKKTHRKQYNNKVD", "down_seq": "ISRRLIWEKNLKYISIHNLE", "snv": [ { "evidence": [ { "id": "rs2525178878", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178878" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806218", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E43", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.62.62", "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": 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": "P43235-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "THWELWKKTHRKQYNNKVDE", "down_seq": "SRRLIWEKNLKYISIHNLEA", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806215", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "I44", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654098874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654098874", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654098874", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654098874#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200870056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200870056", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200870056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200870056", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200870056", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200870056#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200870056", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200870056", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs371277428", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371277428", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371277428", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371277428", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371277428", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371277428#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371277428", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371277428", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654090648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654090648", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WELWKKTHRKQYNNKVDEIS", "down_seq": "RLIWEKNLKYISIHNLEASL", "snv": [ { "evidence": [ { "id": "rs1654098874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654098874" }, { "id": "rs1654098874", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654098874#frequency_tab" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806706", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R46", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200870056", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200870056" }, { "id": "rs200870056", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200870056" }, { "id": "rs200870056", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200870056#frequency_tab" }, { "id": "rs200870056", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200870056" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806208", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R46", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200870056", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200870056" }, { "id": "rs200870056", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200870056" }, { "id": "rs200870056", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200870056#frequency_tab" }, { "id": "rs200870056", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200870056" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806208", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R46", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs371277428", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371277428" }, { "id": "rs371277428", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371277428" }, { "id": "rs371277428", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371277428#frequency_tab" }, { "id": "rs371277428", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371277428" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806209", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R46", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1654090648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654090648" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806210", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R46", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.66.66", "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": 5 } ], "sort_fields": [ "sequence_org", "sequence_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": [ "sequence_org", "sequence_mut", "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": "P43235-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771586535", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771586535", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771586535", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771586535", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771586535", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771586535#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771586535", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771586535", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs199909074", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199909074", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199909074", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199909074", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199909074", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199909074", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199909074", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199909074#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199909074", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199909074", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELWKKTHRKQYNNKVDEISR", "down_seq": "LIWEKNLKYISIHNLEASLG", "snv": [ { "evidence": [ { "id": "rs771586535", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771586535" }, { "id": "rs771586535", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771586535" }, { "id": "rs771586535", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771586535#frequency_tab" }, { "id": "rs771586535", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771586535" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806206", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R47", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs199909074", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199909074" }, { "id": "rs199909074", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199909074" }, { "id": "rs199909074", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199909074" }, { "id": "rs199909074", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199909074#frequency_tab" }, { "id": "rs199909074", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199909074" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806205", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R47", "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", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.67.67", "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": 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": "P43235-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101953599", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953599", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953599", "url": "https://www.ensembl.org/id/rs2101953599", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "WKKTHRKQYNNKVDEISRRL", "down_seq": "WEKNLKYISIHNLEASLGVH", "snv": [ { "evidence": [ { "id": "rs2101953599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953599" }, { "id": "rs2101953599", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953599" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806199", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I49", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.69.69", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1474422274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1474422274", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1474422274", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1474422274", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2525180734", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180734", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MWG", "down_seq": "KVLLLPVVSFALYPEEILDT", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806796", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L4", "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": "rs1474422274", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1474422274" }, { "id": "rs1474422274", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1474422274" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806795", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L4", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2525180734", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525180734" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806801", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L4", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 3, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.24.24", "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": 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": "P43235-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525178794", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178794", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953595", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953595", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953595", "url": "https://www.ensembl.org/id/rs2101953595", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "KKTHRKQYNNKVDEISRRLI", "down_seq": "EKNLKYISIHNLEASLGVHT", "snv": [ { "evidence": [ { "id": "rs2525178794", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178794" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806195", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W50", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2101953595", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953595" }, { "id": "rs2101953595", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953595" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806197", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W50", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806197", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "W50", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 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_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2525178790", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178790", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KTHRKQYNNKVDEISRRLIW", "down_seq": "KNLKYISIHNLEASLGVHTY", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806193", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E51", "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": "rs2525178790", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178790" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806196", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E51", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.71.71", "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": 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": "P43235-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mutations of CTSK result in pycnodysostosis via a reduction in cathepsin K protein.", "journal": "Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research", "date": "1999", "authors": "Ho N, Punturieri A, Wilkin D, Szabo J, Johnson M, Whaley J, Davis J, Clark A, Weiss S, Francomano C", "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" }, { "database": "dbSNP", "id": "rs74315306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315306" }, { "database": "dbSNP", "id": "rs74315305", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315305" } ], "reference": [ { "type": "PubMed", "id": "10491211", "url": "https://glygen.org/publication/PubMed/10491211" } ] } ], "crossref": [ { "id": "rs74315306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315306", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs74315306", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315306#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "10491211", "url": "https://glygen.org/publication/PubMed/10491211", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs2101953982", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953982", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953982", "url": "https://www.ensembl.org/id/rs2101953982", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "THRKQYNNKVDEISRRLIWE", "down_seq": "NLKYISIHNLEASLGVHTYE", "snv": [ { "evidence": [ { "id": "rs74315306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315306" }, { "id": "rs74315306", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315306#frequency_tab" }, { "id": "10491211", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/10491211" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806191", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K52", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs74315306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315306" }, { "id": "rs74315306", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315306#frequency_tab" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806191", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K52", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101953982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953982" }, { "id": "rs2101953982", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953982" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806688", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K52", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43235-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs936779452", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs936779452", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs936779452", "url": "https://www.ncbi.nlm.nih.gov/snp/rs936779452#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs936779452", "url": "http://gnomad.broadinstitute.org/awesome?query=rs936779452", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1557826617", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1557826617", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1557826617", "url": "https://www.ensembl.org/id/rs1557826617", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs764168526", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764168526", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HRKQYNNKVDEISRRLIWEK", "down_seq": "LKYISIHNLEASLGVHTYEL", "snv": [ { "evidence": [ { "id": "rs936779452", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs936779452" }, { "id": "rs936779452", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs936779452#frequency_tab" }, { "id": "rs936779452", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs936779452" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806187", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N53", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1557826617", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1557826617" }, { "id": "rs1557826617", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1557826617" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806186", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N53", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764168526", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764168526" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806193", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N53", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525178672", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178672", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KQYNNKVDEISRRLIWEKNL", "down_seq": "YISIHNLEASLGVHTYELAM", "snv": [ { "evidence": [ { "id": "rs2525178672", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178672" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806182", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K55", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806180", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K55", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.75.75", "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": [ "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": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.56.56", "start_pos": 56, "end_pos": 56, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1236763153", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1236763153", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1236763153", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1236763153#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QYNNKVDEISRRLIWEKNLK", "down_seq": "ISIHNLEASLGVHTYELAMN", "snv": [ { "evidence": [ { "id": "rs1236763153", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1236763153" }, { "id": "rs1236763153", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1236763153#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806178", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y56", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.57.57", "start_pos": 57, "end_pos": 57, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201446793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201446793", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201446793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201446793", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201446793", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201446793#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201446793", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201446793", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2525178648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178648", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "YNNKVDEISRRLIWEKNLKY", "down_seq": "SIHNLEASLGVHTYELAMNH", "snv": [ { "evidence": [ { "id": "rs201446793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201446793" }, { "id": "rs201446793", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201446793" }, { "id": "rs201446793", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201446793#frequency_tab" }, { "id": "rs201446793", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201446793" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806176", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I57", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ] }, { "evidence": [ { "id": "rs2525178648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178648" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806176TA", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I57", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 2 } ], "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": "P43235-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1194794723", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194794723", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1194794723", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194794723#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1194794723", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194794723", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1571127654", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571127654", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571127654", "url": "https://www.ensembl.org/id/rs1571127654", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNKVDEISRRLIWEKNLKYI", "down_seq": "IHNLEASLGVHTYELAMNHL", "snv": [ { "evidence": [ { "id": "rs1194794723", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194794723" }, { "id": "rs1194794723", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194794723#frequency_tab" }, { "id": "rs1194794723", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194794723" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806172", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S58", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1571127654", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571127654" }, { "id": "rs1571127654", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1571127654" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806173", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S58", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.78.78", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "P43235-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MWGL", "down_seq": "VLLLPVVSFALYPEEILDTH", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806793", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K5", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 4, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1301192673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1301192673", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1301192673", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1301192673", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "KVDEISRRLIWEKNLKYISI", "down_seq": "NLEASLGVHTYELAMNHLGD", "snv": [ { "evidence": [ { "id": "rs1301192673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1301192673" }, { "id": "rs1301192673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1301192673" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806166", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H60", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.80.80", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748594586", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748594586", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748594586", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748594586", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748594586", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748594586", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "DEISRRLIWEKNLKYISIHN", "down_seq": "EASLGVHTYELAMNHLGDMT", "snv": [ { "evidence": [ { "id": "rs748594586", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748594586" }, { "id": "rs748594586", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748594586" }, { "id": "rs748594586", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748594586" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806161", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L62", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.82.82", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760640027", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760640027", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ISRRLIWEKNLKYISIHNLE", "down_seq": "SLGVHTYELAMNHLGDMTSE", "snv": [ { "evidence": [ { "id": "rs760640027", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760640027" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806146_150806156", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A64", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.84.84", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1169161020", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1169161020", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1169161020", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1169161020#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1169161020", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1169161020", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRRLIWEKNLKYISIHNLEA", "down_seq": "LGVHTYELAMNHLGDMTSEE", "snv": [ { "evidence": [ { "id": "rs1169161020", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1169161020" }, { "id": "rs1169161020", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1169161020#frequency_tab" }, { "id": "rs1169161020", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1169161020" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806151", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S65", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.85.85", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781761916", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781761916", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781761916", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781761916", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781761916", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781761916", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654088480", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654088480", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654088480", "url": "https://www.ensembl.org/id/rs1654088480", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "RRLIWEKNLKYISIHNLEAS", "down_seq": "GVHTYELAMNHLGDMTSEEV", "snv": [ { "evidence": [ { "id": "rs781761916", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781761916" }, { "id": "rs781761916", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781761916" }, { "id": "rs781761916", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781761916" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806149", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L66", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654088480", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654088480" }, { "id": "rs1654088480", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654088480" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806148", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L66", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.86.86", "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": "P43235-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1419731022", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419731022", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1419731022", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1419731022#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RLIWEKNLKYISIHNLEASL", "down_seq": "VHTYELAMNHLGDMTSEEVV", "snv": [ { "evidence": [ { "id": "rs1419731022", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419731022" }, { "id": "rs1419731022", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1419731022#frequency_tab" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806146", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G67", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.86.86", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755526593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755526593", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755526593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755526593", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755526593", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755526593", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IWEKNLKYISIHNLEASLGV", "down_seq": "TYELAMNHLGDMTSEEVVQK", "snv": [ { "evidence": [ { "id": "rs755526593", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755526593" }, { "id": "rs755526593", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755526593" }, { "id": "rs755526593", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755526593" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806140", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H69", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201086925", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201086925", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201086925", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201086925", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201086925", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201086925", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201086925", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201086925#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201086925", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201086925", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MWGLK", "down_seq": "LLLPVVSFALYPEEILDTHW", "snv": [ { "evidence": [ { "id": "rs201086925", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201086925" }, { "id": "rs201086925", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201086925" }, { "id": "rs201086925", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201086925" }, { "id": "rs201086925", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201086925#frequency_tab" }, { "id": "rs201086925", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201086925" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806790", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "V6", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201086925", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201086925" }, { "id": "rs201086925", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201086925" }, { "id": "rs201086925", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201086925" }, { "id": "rs201086925", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201086925#frequency_tab" }, { "id": "rs201086925", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201086925" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806790", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "V6", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 5, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.26.26", "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": 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": "P43235-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654088048", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654088048", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654088048", "url": "https://www.ensembl.org/id/rs1654088048", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "WEKNLKYISIHNLEASLGVH", "down_seq": "YELAMNHLGDMTSEEVVQKM", "snv": [ { "evidence": [ { "id": "rs1654088048", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654088048" }, { "id": "rs1654088048", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654088048" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806136", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T70", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs780202604", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780202604", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780202604", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780202604", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780202604", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780202604", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs193045250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs193045250", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs193045250", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs193045250", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs193045250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs193045250", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs193045250", "url": "http://gnomad.broadinstitute.org/awesome?query=rs193045250", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EKNLKYISIHNLEASLGVHT", "down_seq": "ELAMNHLGDMTSEEVVQKMT", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs780202604", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780202604" }, { "id": "rs780202604", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780202604" }, { "id": "rs780202604", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780202604" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806132", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y71", "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:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs193045250", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs193045250" }, { "id": "rs193045250", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs193045250" }, { "id": "rs193045250", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs193045250" }, { "id": "rs193045250", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs193045250" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806134", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "Y71", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.91.91", "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": 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": "P43235-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2525178470", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178470", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143688533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143688533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143688533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143688533", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143688533", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143688533#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143688533", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143688533", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KNLKYISIHNLEASLGVHTY", "down_seq": "LAMNHLGDMTSEEVVQKMTG", "snv": [ { "evidence": [ { "id": "rs2525178470", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2525178470" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806131", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E72", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs143688533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143688533" }, { "id": "rs143688533", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143688533" }, { "id": "rs143688533", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143688533#frequency_tab" }, { "id": "rs143688533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143688533" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806129", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E72", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.92.92", "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": 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": "P43235-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1477400707", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1477400707", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1477400707", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1477400707#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1477400707", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1477400707", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "KYISIHNLEASLGVHTYELA", "down_seq": "NHLGDMTSEEVVQKMTGLKV", "snv": [ { "evidence": [ { "id": "rs1477400707", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1477400707" }, { "id": "rs1477400707", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1477400707#frequency_tab" }, { "id": "rs1477400707", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1477400707" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806122", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M75", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.94.94", "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": "P43235-1.76.76", "start_pos": 76, "end_pos": 76, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654087275", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654087275", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654087275", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654087275#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YISIHNLEASLGVHTYELAM", "down_seq": "HLGDMTSEEVVQKMTGLKVP", "snv": [ { "evidence": [ { "id": "rs1654087275", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654087275" }, { "id": "rs1654087275", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654087275#frequency_tab" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806117", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N76", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781761916", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781761916", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781761916", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781761916", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781761916", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781761916", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1363942512", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363942512", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1363942512", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1363942512", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654088480", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654088480", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654088480", "url": "https://www.ensembl.org/id/rs1654088480", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SIHNLEASLGVHTYELAMNH", "down_seq": "GDMTSEEVVQKMTGLKVPLS", "snv": [ { "evidence": [ { "id": "rs781761916", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781761916" }, { "id": "rs781761916", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781761916" }, { "id": "rs781761916", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781761916" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806149", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L78", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1363942512", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363942512" }, { "id": "rs1363942512", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1363942512" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806112", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L78", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654088480", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654088480" }, { "id": "rs1654088480", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654088480" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806148", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L78", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mutations of CTSK result in pycnodysostosis via a reduction in cathepsin K protein.", "journal": "Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research", "date": "1999", "authors": "Ho N, Punturieri A, Wilkin D, Szabo J, Johnson M, Whaley J, Davis J, Clark A, Weiss S, Francomano C", "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" }, { "database": "dbSNP", "id": "rs74315306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315306" }, { "database": "dbSNP", "id": "rs74315305", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315305" } ], "reference": [ { "type": "PubMed", "id": "10491211", "url": "https://glygen.org/publication/PubMed/10491211" } ] } ], "crossref": [ { "id": "rs74315305", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315305", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs74315305", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315305#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "10491211", "url": "https://glygen.org/publication/PubMed/10491211", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs750609110", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750609110", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750609110", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750609110", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750609110", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750609110#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750609110", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750609110", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1419731022", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419731022", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1419731022", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1419731022#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "IHNLEASLGVHTYELAMNHL", "down_seq": "DMTSEEVVQKMTGLKVPLSH", "snv": [ { "evidence": [ { "id": "rs74315305", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74315305" }, { "id": "rs74315305", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs74315305#frequency_tab" }, { "id": "10491211", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/10491211" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806109", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G79", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs750609110", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750609110" }, { "id": "rs750609110", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750609110" }, { "id": "rs750609110", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750609110#frequency_tab" }, { "id": "rs750609110", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750609110" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806110", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G79", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1419731022", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419731022" }, { "id": "rs1419731022", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1419731022#frequency_tab" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806146", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G79", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "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, cathepsins).", "chr_id": "1", "chr_pos": "150806109", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G79", "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": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806110", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G79", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.99.99", "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": 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": 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_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": "P43235-1.7.7", "start_pos": 7, "end_pos": 7, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654101631", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654101631", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654101631", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654101631#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1654101631", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654101631", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1048622635", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1048622635", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1048622635", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1048622635#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MWGLKV", "down_seq": "LLPVVSFALYPEEILDTHWE", "snv": [ { "evidence": [ { "id": "rs1654101631", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654101631" }, { "id": "rs1654101631", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654101631#frequency_tab" }, { "id": "rs1654101631", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1654101631" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806786", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L7", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1048622635", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1048622635" }, { "id": "rs1048622635", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1048622635#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806787", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L7", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 6, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.27.27", "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": 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": "P43235-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1250640636", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250640636", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1250640636", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250640636", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654086866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654086866", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654086866", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654086866#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "NLEASLGVHTYELAMNHLGD", "down_seq": "TSEEVVQKMTGLKVPLSHSR", "snv": [ { "evidence": [ { "id": "rs1250640636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250640636" }, { "id": "rs1250640636", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250640636" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806102", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M81", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654086866", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654086866" }, { "id": "rs1654086866", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654086866#frequency_tab" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806104", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M81", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P43235-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654088048", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654088048", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654088048", "url": "https://www.ensembl.org/id/rs1654088048", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs145693431", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145693431", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145693431", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145693431", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145693431", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145693431#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145693431", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145693431", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LEASLGVHTYELAMNHLGDM", "down_seq": "SEEVVQKMTGLKVPLSHSRS", "snv": [ { "evidence": [ { "id": "rs1654088048", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654088048" }, { "id": "rs1654088048", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654088048" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806136", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T82", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs145693431", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145693431" }, { "id": "rs145693431", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145693431" }, { "id": "rs145693431", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145693431#frequency_tab" }, { "id": "rs145693431", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145693431" } ], "glycoeffect": [], "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806016", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T82", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.102.102", "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": 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": "P43235-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs143688533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143688533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143688533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143688533", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143688533", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143688533#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143688533", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143688533", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654084532", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654084532", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654084532", "url": "https://www.ensembl.org/id/rs1654084532", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ASLGVHTYELAMNHLGDMTS", "down_seq": "EVVQKMTGLKVPLSHSRSND", "snv": [ { "evidence": [ { "id": "rs143688533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143688533" }, { "id": "rs143688533", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143688533" }, { "id": "rs143688533", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143688533#frequency_tab" }, { "id": "rs143688533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143688533" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806129", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E84", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654084532", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654084532" }, { "id": "rs1654084532", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654084532" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806010", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E84", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.104.104", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "P43235-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101953352", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953352", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953352", "url": "https://www.ensembl.org/id/rs2101953352", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2101953350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953350", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101953350", "url": "https://www.ensembl.org/id/rs2101953350", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SLGVHTYELAMNHLGDMTSE", "down_seq": "VVQKMTGLKVPLSHSRSNDT", "snv": [ { "evidence": [ { "id": "rs2101953352", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953352" }, { "id": "rs2101953352", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953352" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806007", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E85", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2101953350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101953350" }, { "id": "rs2101953350", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101953350" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806006", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E85", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.105.105", "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": 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": "P43235-1.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654084358", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654084358", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654084358", "url": "https://www.ensembl.org/id/rs1654084358", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LGVHTYELAMNHLGDMTSEE", "down_seq": "VQKMTGLKVPLSHSRSNDTL", "snv": [ { "evidence": [ { "id": "rs1654084358", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654084358" }, { "id": "rs1654084358", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1654084358" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806004", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V86", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.105.105", "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": "P43235-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs762212949", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762212949", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762212949", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762212949", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762212949", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762212949#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762212949", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762212949", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "VHTYELAMNHLGDMTSEEVV", "down_seq": "KMTGLKVPLSHSRSNDTLYI", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805996", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q88", "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" ] }, { "evidence": [ { "id": "rs762212949", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762212949" }, { "id": "rs762212949", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762212949" }, { "id": "rs762212949", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762212949#frequency_tab" }, { "id": "rs762212949", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762212949" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805997", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q88", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs762212949", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762212949" }, { "id": "rs762212949", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762212949" }, { "id": "rs762212949", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762212949#frequency_tab" }, { "id": "rs762212949", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762212949" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805997", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q88", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.108.108", "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": 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": "P43235-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MWGLKVL", "down_seq": "LPVVSFALYPEEILDTHWEL", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150806784", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L8", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": 7, "direction": "downstream", "id": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.28.28", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1479943290", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1479943290", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1479943290", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1479943290", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs777061480", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777061480", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777061480", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777061480", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777061480", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777061480#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777061480", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777061480", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "TYELAMNHLGDMTSEEVVQK", "down_seq": "TGLKVPLSHSRSNDTLYIPE", "snv": [ { "evidence": [ { "id": "rs1479943290", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1479943290" }, { "id": "rs1479943290", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1479943290" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805991", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M90", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs777061480", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777061480" }, { "id": "rs777061480", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777061480" }, { "id": "rs777061480", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777061480#frequency_tab" }, { "id": "rs777061480", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777061480" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805992", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M90", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.110.110", "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": "P43235-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1269158585", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1269158585", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1269158585", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1269158585", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YELAMNHLGDMTSEEVVQKM", "down_seq": "GLKVPLSHSRSNDTLYIPEW", "snv": [ { "evidence": [ { "id": "rs1269158585", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1269158585" }, { "id": "rs1269158585", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1269158585" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805988", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T91", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P43235-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768992778", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768992778", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs768992778", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768992778", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768992778", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768992778", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1327075509", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1327075509", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1327075509", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1327075509#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1327075509", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1327075509", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "ELAMNHLGDMTSEEVVQKMT", "down_seq": "LKVPLSHSRSNDTLYIPEWE", "snv": [ { "evidence": [ { "id": "rs768992778", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768992778" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805986", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G92", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805985", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "G92", "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": "rs768992778", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768992778" }, { "id": "rs768992778", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768992778" }, { "id": "rs768992778", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768992778" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805986", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G92", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1327075509", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1327075509" }, { "id": "rs1327075509", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1327075509#frequency_tab" }, { "id": "rs1327075509", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1327075509" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805985", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G92", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.112.112", "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": 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": "P43235-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AMNHLGDMTSEEVVQKMTGL", "down_seq": "VPLSHSRSNDTLYIPEWEGR", "snv": [ { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805980", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K94", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.114.114", "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": "P43235-1.96.96", "start_pos": 96, "end_pos": 96, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1286298605", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1286298605", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1286298605", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1286298605#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1286298605", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1286298605", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1654083163", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654083163", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1654083163", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654083163#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P43235", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NHLGDMTSEEVVQKMTGLKV", "down_seq": "LSHSRSNDTLYIPEWEGRAP", "snv": [ { "evidence": [ { "id": "rs1286298605", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1286298605" }, { "id": "rs1286298605", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1286298605#frequency_tab" }, { "id": "rs1286298605", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1286298605" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805974", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P96", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1654083163", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654083163" }, { "id": "rs1654083163", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1654083163#frequency_tab" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805973", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P96", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P43235", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P43235" }, { "id": "rs1286298605", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1286298605" }, { "id": "rs1286298605", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1286298605#frequency_tab" }, { "id": "rs1286298605", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1286298605" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, cathepsins).", "chr_id": "1", "chr_pos": "150805974", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P96", "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": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.116.116", "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": 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": "P43235-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1654082906", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654082906", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773943327", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773943327", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "HLGDMTSEEVVQKMTGLKVP", "down_seq": "SHSRSNDTLYIPEWEGRAPD", "snv": [ { "evidence": [ { "id": "rs1654082906", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1654082906" }, { "id": "rs773943327", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773943327" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805970", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L97", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.117.117", "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": [ "sequence_org", "sequence_mut", "comment", "chr_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": "P43235-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs587742006", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587742006", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs587742006", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587742006", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs587742006", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587742006", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs587742006", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587742006", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GDMTSEEVVQKMTGLKVPLS", "down_seq": "SRSNDTLYIPEWEGRAPDSV", "snv": [ { "evidence": [ { "id": "rs587742006", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587742006" }, { "id": "rs587742006", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587742006" }, { "id": "rs587742006", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587742006" }, { "id": "rs587742006", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587742006" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805965", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H99", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs587742006", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587742006" }, { "id": "rs587742006", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs587742006" }, { "id": "rs587742006", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587742006" }, { "id": "rs587742006", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587742006" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150805965", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H99", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P43235-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P43235-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43235-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43235-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43235-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43235-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43235-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43235-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43235-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43235-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43235-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43235-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43235-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43235-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43235-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.117.117", "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": 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": "P43235-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "P43235-1", "length": 329, "uniprot_id": "CATK_HUMAN", "protein_name": "Cathepsin K", "refseq_ac": "NP_000387", "refseq_name": "cathepsin K preproprotein", "gene_name": "CTSK", "gene_names_uniprotkb": "CTSK; CTSO2; CTSO", "gene_names_refseq": "CTS02; CTSK; CTSO1; CTSO2; CTSO; PKND; PYCD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P43235", "url": "https://www.uniprot.org/uniprotkb/P43235" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1057517252", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057517252", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1057517252", "url": "https://www.ensembl.org/id/rs1057517252", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1395649142", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395649142", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1395649142", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1395649142#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1395649142", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1395649142", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1553197476", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553197476", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MWGLKVLL", "down_seq": "PVVSFALYPEEILDTHWELW", "snv": [ { "evidence": [ { "id": "rs1057517252", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057517252" }, { "id": "rs1057517252", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1057517252" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806780", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L9", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1395649142", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395649142" }, { "id": "rs1395649142", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1395649142#frequency_tab" }, { "id": "rs1395649142", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1395649142" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806781", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L9", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1553197476", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553197476" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, cathepsins.", "chr_id": "1", "chr_pos": "150806782CAG", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L9", "disease": [ { "disease_id": "DOID:0080038", "recommended_name": { "id": "DOID:0080038", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080038", "name": "pycnodysostosis", "description": "An osteochondrodysplasia that has_material_basis_in a mutation in the CTSK gene which results_in dwarfism, brittle bones, osteopetrosis, shortening of the distal phalanges." }, "synonyms": [ { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "Pycnodysostosis is a genetic lysosomal disease characterized by short stature, increased density of the bones (osteosclerosis/osteopetrosis), and brittle bones. Other features may include underdevelopment of the tips of the fingers with absent or small nails, an abnormal collarbone (clavicle), distinctive facial features including a large head with a small face and chin, underdeveloped facial bones, a high forehead, and dental abnormalities.Pycnodysostosis is an autosomal recessive condition caused by mutations in the gene that codes the enzyme cathepsin K (CTSK) on chromosome 1q21. The diagnosis of pycnodysostosis is based on physical features and X-ray findings. Molecular genetic testing is available. Treatment should address the symptoms found in each patient and may include orthopedic monitoring, treatment of fractures, appropriate dental care, and craniofacial surgery." }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "Pyknodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "pycnodysostosis", "description": "" }, { "id": "MONDO:0009940", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009940", "name": "PKND", "description": "" }, { "id": "MIM:265800", "resource": "MIM", "url": "https://www.omim.org/entry/265800", "name": "Pycnodysostosis", "description": "Pycnodysostosis" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080038", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080038" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "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": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "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": "166", "end_pos": "166" }, { "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": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "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": "187", "end_pos": "187" }, { "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": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "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": "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": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "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": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "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": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "298", "end_pos": "298" }, { "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": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "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": "316", "end_pos": "316" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "33", "end_pos": "33" }, { "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": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "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": "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": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "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": "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": "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": "P43235-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43235-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43235-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43235-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43235-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43235-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43235-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43235-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43235-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43235-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43235-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43235-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43235-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43235-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43235-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43235-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43235-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43235-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43235-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43235-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43235-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43235-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43235-1.29.29", "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": 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": 2 } ], "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": "Q5EG05-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "Q5EG05-1", "length": 197, "uniprot_id": "CAR16_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 16", "refseq_ac": "NP_443121", "refseq_name": "caspase recruitment domain-containing protein 16 isoform 2", "gene_name": "CARD16", "gene_names_uniprotkb": "CARD16; COP1; COP", "gene_names_refseq": "CARD16; COP1; COP; LLID-114769; PSEUDO-ICE", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5EG05", "url": "https://www.uniprot.org/uniprotkb/Q5EG05" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5EG05", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5EG05", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EKVKRENATVMDKTRALIDS", "down_seq": "IPKGAQACQICITYICEEDS", "snv": [ { "evidence": [ { "id": "Q5EG05", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5EG05" } ], "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": "11", "chr_pos": "105044485", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V61", "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": "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": "Q5JPI3-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q5JPI3-1", "length": 329, "uniprot_id": "CC038_HUMAN", "protein_name": "Uncharacterized protein C3orf38", "refseq_ac": "NP_776185", "refseq_name": "uncharacterized protein C3orf38", "gene_name": "C3orf38", "gene_names_uniprotkb": "C3orf38", "gene_names_refseq": "C3orf38", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5JPI3", "url": "https://www.uniprot.org/uniprotkb/Q5JPI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q5JPI3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5JPI3" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] }, { "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": "Q5JPI3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5JPI3" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5JPI3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5JPI3", "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": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "Q5JPI3", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5JPI3" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "173", "end_pos": "173" }, { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "32", "end_pos": "32" } ] } ], "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": "Q5JPI3-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "Q5JPI3-1", "length": 329, "uniprot_id": "CC038_HUMAN", "protein_name": "Uncharacterized protein C3orf38", "refseq_ac": "NP_776185", "refseq_name": "uncharacterized protein C3orf38", "gene_name": "C3orf38", "gene_names_uniprotkb": "C3orf38", "gene_names_refseq": "C3orf38", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5JPI3", "url": "https://www.uniprot.org/uniprotkb/Q5JPI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5JPI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5JPI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "LNSQNPFLGPPQDEWGPQHF", "down_seq": "HDVKLRFYYNTSEQNVMDYH", "snv": [ { "evidence": [ { "id": "Q5JPI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5JPI3" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "88156164", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "W173", "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: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": "173", "end_pos": "173" }, { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "32", "end_pos": "32" } ] } ], "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": "Q5JPI3-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "Q5JPI3-1", "length": 329, "uniprot_id": "CC038_HUMAN", "protein_name": "Uncharacterized protein C3orf38", "refseq_ac": "NP_776185", "refseq_name": "uncharacterized protein C3orf38", "gene_name": "C3orf38", "gene_names_uniprotkb": "C3orf38", "gene_names_refseq": "C3orf38", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5JPI3", "url": "https://www.uniprot.org/uniprotkb/Q5JPI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5JPI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5JPI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YYNTSEQNVMDYHGAEIVSL", "down_seq": "LLSLVKEEFLFLSPNLDSHG", "snv": [ { "evidence": [ { "id": "Q5JPI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5JPI3" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "88156247", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R201", "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: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": "173", "end_pos": "173" }, { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "32", "end_pos": "32" } ] } ], "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": "Q5JPI3-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "Q5JPI3-1", "length": 329, "uniprot_id": "CC038_HUMAN", "protein_name": "Uncharacterized protein C3orf38", "refseq_ac": "NP_776185", "refseq_name": "uncharacterized protein C3orf38", "gene_name": "C3orf38", "gene_names_uniprotkb": "C3orf38", "gene_names_refseq": "C3orf38", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5JPI3", "url": "https://www.uniprot.org/uniprotkb/Q5JPI3" } ], "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": "Q5JPI3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5JPI3-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q5JPI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5JPI3", "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": "EGCRNLLGLLDNDEIMALCD", "down_seq": "VTNRLVQPQDRQDAVHAILA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q5JPI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5JPI3" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr32" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "173", "end_pos": "173" }, { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "32", "end_pos": "32" } ] } ], "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": "Q66K79-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs760780373", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760780373", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760780373", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760780373", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760780373", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760780373#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760780373", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760780373", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs147806032", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147806032", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs147806032", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147806032", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs147806032", "url": "https://www.ncbi.nlm.nih.gov/snp/rs147806032#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs147806032", "url": "http://gnomad.broadinstitute.org/awesome?query=rs147806032", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LAQYLCSEYLLGNPRIQRLL", "down_seq": "TTRIHLLPSMNPDGYEVAAA", "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": "Asn281", "evidence": [ { "id": "Q66K79", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q66K79#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs760780373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760780373" }, { "id": "rs760780373", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760780373" }, { "id": "rs760780373", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760780373#frequency_tab" }, { "id": "rs760780373", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760780373" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->DTT).", "chr_id": "4", "chr_pos": "8606120", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N281", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs147806032", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147806032" }, { "id": "rs147806032", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147806032" }, { "id": "rs147806032", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs147806032#frequency_tab" }, { "id": "rs147806032", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs147806032" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->TTT).", "chr_id": "4", "chr_pos": "8606121", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N281", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760780373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760780373" }, { "id": "rs760780373", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760780373" }, { "id": "rs760780373", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760780373#frequency_tab" }, { "id": "rs760780373", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760780373" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->YTT).", "chr_id": "4", "chr_pos": "8606120", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N281", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q66K79-1.275.275", "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" ] }, { "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": "Q66K79-1.405.405", "start_pos": 405, "end_pos": 405, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "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": "rs371735226", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371735226", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs371735226", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371735226", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371735226", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371735226#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371735226", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371735226", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs371735226", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371735226", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VVSYPFDFSKHPQEEKMFSP", "down_seq": "PDEKMFKLLSRAYADVHPMM", "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": "Thr405", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs371735226", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371735226" } ], "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": "4", "chr_pos": "8607412", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T405", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" }, { "id": "rs371735226", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371735226" }, { "id": "rs371735226", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371735226" }, { "id": "rs371735226", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371735226#frequency_tab" }, { "id": "rs371735226", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371735226" }, { "id": "rs371735226", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371735226" } ], "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: o-glyco-site-loss (T->M).", "chr_id": "4", "chr_pos": "8607412", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T405", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q66K79-1.391.391", "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": "Q66K79-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs564816856", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs564816856", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs564816856", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs564816856", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs564816856", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs564816856", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs564816856", "url": "http://gnomad.broadinstitute.org/awesome?query=rs564816856", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LGCAVLAPRCEGGWVRRPCR", "down_seq": "ICEGLREVCQPAFDAIDMAW", "snv": [ { "evidence": [ { "id": "rs564816856", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs564816856" }, { "id": "rs564816856", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs564816856" }, { "id": "rs564816856", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs564816856" }, { "id": "rs564816856", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs564816856" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HIC->NIC).", "chr_id": "4", "chr_pos": "8601359", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H120", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q66K79-1.135.135", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RRPCRHICEGLREVCQPAFD", "down_seq": "IDMAWPYFLDCHRYFTREDE", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "8601404", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A135", "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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q66K79-1.120.120", "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": "Q66K79-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LRGGLEADEALPSGLPPTFI", "down_seq": "FSHHSYAQMVRVLRRTASRC", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "8604030", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R184", "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: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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "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": "Q66K79-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FSHHSYAQMVRVLRRTASRC", "down_seq": "HVARTYSIGRSFDGRELLVI", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "8604092", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A205", "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: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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "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": "Q66K79-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "REMLIYLAQYLCSEYLLGNP", "down_seq": "IQRLLNTTRIHLLPSMNPDG", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "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 (5).", "chr_id": "4", "chr_pos": "8606103", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R275", "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: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: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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q66K79-1.281.281", "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": "Q66K79-1.326.326", "start_pos": 326, "end_pos": 326, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750663941", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750663941", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750663941", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750663941", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750663941", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750663941#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750663941", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750663941", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YNGWTSGRQNAQNLDLNRNF", "down_seq": "DLTSEYYRLAETRGARSDHI", "snv": [ { "evidence": [ { "id": "rs750663941", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750663941" }, { "id": "rs750663941", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750663941" }, { "id": "rs750663941", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750663941#frequency_tab" }, { "id": "rs750663941", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750663941" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFP->NFS).", "chr_id": "4", "chr_pos": "8606806", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P326", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750663941", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750663941" }, { "id": "rs750663941", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750663941" }, { "id": "rs750663941", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750663941#frequency_tab" }, { "id": "rs750663941", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750663941" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFP->NFT).", "chr_id": "4", "chr_pos": "8606806", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P326", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "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": "Q66K79-1.391.391", "start_pos": 391, "end_pos": 391, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs144181545", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144181545", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs144181545", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144181545", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs144181545", "url": "https://www.ncbi.nlm.nih.gov/snp/rs144181545#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs144181545", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs144181545", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs144181545", "url": "http://gnomad.broadinstitute.org/awesome?query=rs144181545", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IPFVLSASLHGGDLVVSYPF", "down_seq": "FSKHPQEEKMFSPTPDEKMF", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" }, { "id": "rs144181545", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144181545" }, { "id": "rs144181545", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144181545" }, { "id": "rs144181545", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs144181545#frequency_tab" }, { "id": "rs144181545", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs144181545" }, { "id": "rs144181545", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs144181545" } ], "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 (DFS->NFS).", "chr_id": "4", "chr_pos": "8607369", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D391", "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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q66K79-1.405.405", "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": "Q66K79-1.447.447", "start_pos": 447, "end_pos": 447, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752287558", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287558", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752287558", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287558", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752287558", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752287558", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DRSENRCGGNFLKRGSIING", "down_seq": "DWYSFTGGMSDFNYLHTNCF", "snv": [ { "evidence": [ { "id": "rs752287558", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287558" }, { "id": "rs752287558", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287558" }, { "id": "rs752287558", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752287558" } ], "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": "4", "chr_pos": "8612138", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A447", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q66K79-1.467.467", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.467.467", "start_pos": 467, "end_pos": 467, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1715983629", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1715983629", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1715983629", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1715983629", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "ADWYSFTGGMSDFNYLHTNC", "down_seq": "EITVELGCVKFPPEEALYIL", "snv": [ { "evidence": [ { "id": "rs1715983629", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1715983629" }, { "id": "rs1715983629", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1715983629" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCF->NCS).", "chr_id": "4", "chr_pos": "8614395", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F467", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q66K79-1.447.447", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q66K79-1.478.478", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.478.478", "start_pos": 478, "end_pos": 478, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "DFNYLHTNCFEITVELGCVK", "down_seq": "PPEEALYILWQHNKESLLNF", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "8614428", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F478", "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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q66K79-1.467.467", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q66K79-1.492.492", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.492.492", "start_pos": 492, "end_pos": 492, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1371154614", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1371154614", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1371154614", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1371154614#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1371154614", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1371154614", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ELGCVKFPPEEALYILWQHN", "down_seq": "ESLLNFVETVHRGIKGVVTD", "snv": [ { "evidence": [ { "id": "rs1371154614", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1371154614" }, { "id": "rs1371154614", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1371154614#frequency_tab" }, { "id": "rs1371154614", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1371154614" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KES->NES).", "chr_id": "4", "chr_pos": "8614471", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K492", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q66K79-1.478.478", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.529.529", "start_pos": 529, "end_pos": 529, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VVTDKFGKPVKNARISVKGI", "down_seq": "HDITTAPDGDYWRLLPPGIH", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "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 (6).", "chr_id": "4", "chr_pos": "8618511", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R529", "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: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: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: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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q66K79-1.531.531", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.531.531", "start_pos": 531, "end_pos": 531, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751421093", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751421093", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751421093", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751421093", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751421093", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751421093#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751421093", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751421093", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TDKFGKPVKNARISVKGIRH", "down_seq": "ITTAPDGDYWRLLPPGIHIV", "snv": [ { "evidence": [ { "id": "rs751421093", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751421093" }, { "id": "rs751421093", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751421093" }, { "id": "rs751421093", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751421093#frequency_tab" }, { "id": "rs751421093", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751421093" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DIT->NIT).", "chr_id": "4", "chr_pos": "8618516", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D531", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q66K79-1.529.529", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PPAADSATCVDLQLRTCSDA", "down_seq": "YNHTTFPNLLQHRSWEVVEA", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "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": "4", "chr_pos": "8601164", "ref_nt": "G", "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" } ] }, { "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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q66K79-1.58.58", "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": "Q66K79-1.569.569", "start_pos": 569, "end_pos": 569, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HIVIAQAPGYAKVIKKVIIP", "down_seq": "RMKRAGRVDFILQPLGMGPK", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "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": "4", "chr_pos": "8619363", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A569", "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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q66K79-1.576.576", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.576.576", "start_pos": 576, "end_pos": 576, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PGYAKVIKKVIIPARMKRAG", "down_seq": "VDFILQPLGMGPKNFIHGLR", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "8619384", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R576", "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: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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q66K79-1.569.569", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q66K79-1.592.592", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs202061891", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202061891", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202061891", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202061891", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs202061891", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202061891#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs202061891", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202061891", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "ADSATCVDLQLRTCSDAAYN", "down_seq": "TTFPNLLQHRSWEVVEASSE", "snv": [ { "evidence": [ { "id": "rs202061891", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202061891" }, { "id": "rs202061891", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202061891" }, { "id": "rs202061891", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202061891#frequency_tab" }, { "id": "rs202061891", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202061891" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HTT->NTT).", "chr_id": "4", "chr_pos": "8601173", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H58", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q66K79-1.55.55", "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": "Q66K79-1.592.592", "start_pos": 592, "end_pos": 592, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs955767615", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955767615", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs955767615", "url": "http://gnomad.broadinstitute.org/awesome?query=rs955767615", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KRAGRVDFILQPLGMGPKNF", "down_seq": "HGLRRTGPHDPLGGASSLGE", "snv": [ { "evidence": [ { "id": "rs955767615", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955767615" }, { "id": "rs955767615", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs955767615" } ], "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": "4", "chr_pos": "8619433", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I592", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q66K79-1.576.576", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q66K79-1.598.598", "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": "Q66K79-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MPPP", "down_seq": "PLLLLTVLVVAAARPGCEFE", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "10", "frequency": "0.2", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: patient count (10/4799).", "chr_id": "4", "chr_pos": "8592847", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L5", "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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "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": "Q66K79-1.626.626", "start_pos": 626, "end_pos": 626, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GASSLGEATEPDPLRARRQP", "down_seq": "ADGSKPWWWSYFTSLSTHRP", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "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": "4", "chr_pos": "8619535", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S626", "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: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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q66K79-1.628.628", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.628.628", "start_pos": 628, "end_pos": 628, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs751803458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751803458", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751803458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751803458", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751803458", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751803458#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751803458", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751803458", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs751803458", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs751803458", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SSLGEATEPDPLRARRQPSA", "down_seq": "GSKPWWWSYFTSLSTHRPRW", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" }, { "id": "rs751803458", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751803458" }, { "id": "rs751803458", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751803458" }, { "id": "rs751803458", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751803458#frequency_tab" }, { "id": "rs751803458", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751803458" }, { "id": "rs751803458", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs751803458" } ], "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 (DGS->NGS).", "chr_id": "4", "chr_pos": "8619540", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D628", "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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q66K79-1.626.626", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q66K79-1.652.652", "start_pos": 652, "end_pos": 652, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PWWWSYFTSLSTHRPRWLLK", "down_seq": "", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Y", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "8619612", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y652", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "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": "Q66K79-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q66K79", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "WEVVEASSEYILLSVLHQLL", "down_seq": "GQCNPDLRLLGCAVLAPRCE", "snv": [ { "evidence": [ { "id": "Q66K79", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q66K79" } ], "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": "4", "chr_pos": "8601269", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E90", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "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": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "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": "Q66K79-1.598.598", "start_pos": 598, "end_pos": 598, "uniprot_canonical_ac": "Q66K79-1", "length": 652, "uniprot_id": "CBPZ_HUMAN", "protein_name": "Carboxypeptidase Z", "refseq_ac": "NP_001014447", "refseq_name": "carboxypeptidase Z isoform 1 precursor", "gene_name": "CPZ", "gene_names_uniprotkb": "CPZ", "gene_names_refseq": "CPZ", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q66K79", "url": "https://www.uniprot.org/uniprotkb/Q66K79" } ], "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": "Q66K79", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q66K79" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q66K79", "url": "https://www.iedb.org/epitope/Q66K79", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q66K79", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q66K79", "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": "DFILQPLGMGPKNFIHGLRR", "down_seq": "GPHDPLGGASSLGEATEPDP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q66K79", "url": "https://www.iedb.org/epitope/Q66K79" }, { "database": "iPTMnet", "id": "Q66K79", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q66K79" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr598" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "281", "end_pos": "281" }, { "start_pos": "405", "end_pos": "405" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "598", "end_pos": "598" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q66K79-1.592.592", "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": "Q6NZI2-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "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": "Q6NZI2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q6NZI2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Z-band alternatively spliced PDZ motif protein (ZASP) is the major O-linked beta-N-acetylglucosamine-substituted protein in human heart myofibrils.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Leung MC, Hitchen PG, Ward DG, Messer AE, Marston SB", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6NZI2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "23271734", "url": "https://glygen.org/publication/PubMed/23271734" } ] }, { "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": "Q6NZI2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2" }, { "database": "O-GlcNAc Atlas", "id": "Q6NZI2", "url": "https://oglcnac.org/atlas/detail/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "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": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23271734", "url": "https://glygen.org/publication/PubMed/23271734", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "https://oglcnac.org/atlas/detail/Q6NZI2", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SGLRRVDDFKKAFSKEKMEK", "down_seq": "KVRTRENLEKTRLKTKENLE", "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": "Thr244", "evidence": [ { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q6NZI2", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6NZI2" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "23271734", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23271734" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q6NZI2", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6NZI2" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q6NZI2-1.247.247", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1328937078", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1328937078", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1328937078", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1328937078#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAVQSIQGELSKLGKAHATT", "down_seq": "NTVSKLLEKVRKVSVNVKTV", "snv": [ { "evidence": [ { "id": "rs1328937078", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1328937078" }, { "id": "rs1328937078", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1328937078#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 (SNT->NNT).", "chr_id": "17", "chr_pos": "42422787", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S104", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q6NZI2-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6NZI2-1.118.118", "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": "Q6NZI2-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs777309097", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777309097", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777309097", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777309097", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777309097", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777309097#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777309097", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777309097", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LGKAHATTSNTVSKLLEKVR", "down_seq": "VSVNVKTVRGSLERQAGQIK", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" }, { "id": "rs777309097", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777309097" }, { "id": "rs777309097", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777309097" }, { "id": "rs777309097", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777309097#frequency_tab" }, { "id": "rs777309097", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777309097" } ], "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 (KVS->NVS).", "chr_id": "17", "chr_pos": "42422750", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K116", "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": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6NZI2-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.118.118", "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": "Q6NZI2-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1205263846", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205263846", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1205263846", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205263846", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TVRGSLERQAGQIKKLEVNE", "down_seq": "ELLRRRNFKVMIYQDEVKLP", "snv": [ { "evidence": [ { "id": "rs1205263846", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205263846" }, { "id": "rs1205263846", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205263846" } ], "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": "17", "chr_pos": "42422671", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A143", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q6NZI2-1.156.156", "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": "Q6NZI2-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2085437686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2085437686", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2085437686", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2085437686#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522", "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": "RNFKVMIYQDEVKLPAKLSI", "down_seq": "KSLKESEALPEKEGEELGEG", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" }, { "id": "rs2085437686", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2085437686" }, { "id": "rs2085437686", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2085437686#frequency_tab" } ], "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 (SKS->NKS).", "chr_id": "17", "chr_pos": "42405354", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S169", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser169" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6NZI2-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.167.167", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6NZI2-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6NZI2-1.175.175", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VMIYQDEVKLPAKLSISKSL", "down_seq": "ESEALPEKEGEELGEGERPE", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KES->NES).", "chr_id": "17", "chr_pos": "42405341", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K173", "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": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6NZI2-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6NZI2-1.167.167", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6NZI2-1.169.169", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.175.175", "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": "Q6NZI2-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "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": "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGEELGEGERPEEDAAALEL", "down_seq": "SDEAVEVEEVIEESRAERIK", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "42405255", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S202", "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: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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser202" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6NZI2-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6NZI2-1.216.216", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6NZI2-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6NZI2-1.220.220", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ALELSSDEAVEVEEVIEESR", "down_seq": "ERIKRSGLRRVDDFKKAFSK", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "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 (4).", "chr_id": "17", "chr_pos": "42405208", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A218", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6NZI2-1.202.202", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q6NZI2-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.216.216", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.220.220", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6NZI2-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELSSDEAVEVEEVIEESRAE", "down_seq": "IKRSGLRRVDDFKKAFSKEK", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "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": "42405202", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R220", "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": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6NZI2-1.202.202", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q6NZI2-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6NZI2-1.216.216", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.218.218", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6NZI2-1.247.247", "start_pos": 247, "end_pos": 247, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RRVDDFKKAFSKEKMEKTKV", "down_seq": "TRENLEKTRLKTKENLEKTR", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "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": "17", "chr_pos": "42405120", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R247", "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: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: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": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q6NZI2-1.244.244", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6NZI2-1.266.266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6NZI2-1.266.266", "start_pos": 266, "end_pos": 266, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VRTRENLEKTRLKTKENLEK", "down_seq": "RHTLEKRMNKLGTRLVPAER", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "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": "42405063", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T266", "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: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": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6NZI2-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6NZI2-1.279.279", "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": "Q6NZI2-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GTRLVPAERREKLKTSRDKL", "down_seq": "KSFTPDHVVYARSKTAVYKV", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "glycoeffect": [], "subjects_tested": "2003", "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": "42404967", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R298", "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: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": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6NZI2-1.279.279", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6NZI2-1.302.302", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6NZI2-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6NZI2-1.314.314", "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": "Q6NZI2-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RDKLRKSFTPDHVVYARSKT", "down_seq": "VYKVPPFTFHVKKIREGQVE", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "42404919", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A314", "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: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: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": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6NZI2-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q6NZI2-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q6NZI2-1.302.302", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6NZI2-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6NZI2-1.329.329", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6NZI2-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ARSKTAVYKVPPFTFHVKKI", "down_seq": "EGQVEVLKATEMVEVGADDD", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "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": "17", "chr_pos": "42404875", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R329", "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": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6NZI2-1.314.314", "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": "Q6NZI2-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1423821820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1423821820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1423821820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1423821820", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "PSSAGAQAAEEPSGAGSEEL", "down_seq": "KSDQVNGVLVLSLLDKIIGA", "snv": [ { "evidence": [ { "id": "rs1423821820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1423821820" }, { "id": "rs1423821820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1423821820" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IKS->NKS).", "chr_id": "17", "chr_pos": "42422967", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I44", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6NZI2-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6NZI2-1.40.40", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.46.46", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6NZI2-1.60.60", "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": "Q6NZI2-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SEELIKSDQVNGVLVLSLLD", "down_seq": "IIGAVDQIQLTQAQLEERQA", "snv": [ { "evidence": [ { "id": "Q6NZI2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6NZI2" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "K", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "42422920", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K60", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6NZI2-1.40.40", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q6NZI2-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q6NZI2-1.46.46", "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": "Q6NZI2-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis.", "journal": "Analytical chemistry", "date": "2008", "authors": "Wang B, Malik R, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KAHATTSNTVSKLLEKVRKV", "down_seq": "VNVKTVRGSLERQAGQIKKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ], "site_lbl": "Ser118" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6NZI2-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.116.116", "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": "Q6NZI2-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Effects of HER2 overexpression on cell signaling networks governing proliferation and migration.", "journal": "Molecular systems biology", "date": "2006", "authors": "Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova V, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" } ] }, { "title": "Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" } ] }, { "title": "Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.", "journal": "Journal of proteome research", "date": "2008", "authors": "Tsai CF, Wang YT, Chen YR, Lai CY, Lin PY, Pan KT, Chen JY, Khoo KH, Chen YJ", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KKLEVNEAELLRRRNFKVMI", "down_seq": "QDEVKLPAKLSISKSLKESE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" }, { "database": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ], "site_lbl": "Tyr156" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6NZI2-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6NZI2-1.167.167", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6NZI2-1.169.169", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6NZI2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6NZI2-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6NZI2-1.175.175", "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": "Q6NZI2-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages.", "journal": "Journal of proteome research", "date": "2009", "authors": "Malik R, Lenobel R, Santamaria A, Ries A, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "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": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289", "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": "RRRNFKVMIYQDEVKLPAKL", "down_seq": "ISKSLKESEALPEKEGEELG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "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": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser167" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6NZI2-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.169.169", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6NZI2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6NZI2-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6NZI2-1.175.175", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "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": "FKVMIYQDEVKLPAKLSISK", "down_seq": "LKESEALPEKEGEELGEGER", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser171" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6NZI2-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6NZI2-1.167.167", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.169.169", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6NZI2-1.175.175", "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": "Q6NZI2-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "IYQDEVKLPAKLSISKSLKE", "down_seq": "EALPEKEGEELGEGERPEED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser175" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6NZI2-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6NZI2-1.167.167", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6NZI2-1.169.169", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6NZI2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.173.173", "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": "Q6NZI2-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "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": "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GEELGEGERPEEDAAALELS", "down_seq": "DEAVEVEEVIEESRAERIKR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser203" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6NZI2-1.202.202", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6NZI2-1.216.216", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6NZI2-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6NZI2-1.220.220", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "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": "AAALELSSDEAVEVEEVIEE", "down_seq": "RAERIKRSGLRRVDDFKKAF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser216" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6NZI2-1.202.202", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6NZI2-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6NZI2-1.220.220", "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": "Q6NZI2-1.279.279", "start_pos": 279, "end_pos": 279, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.iedb.org/epitope/Q6NZI2", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "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": "TKENLEKTRHTLEKRMNKLG", "down_seq": "RLVPAERREKLKTSRDKLRK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q6NZI2", "url": "https://www.iedb.org/epitope/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr279" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6NZI2-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6NZI2-1.298.298", "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": "Q6NZI2-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "title": "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis.", "journal": "Analytical chemistry", "date": "2008", "authors": "Wang B, Malik R, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages.", "journal": "Journal of proteome research", "date": "2009", "authors": "Malik R, Lenobel R, Santamaria A, Ries A, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "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": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RLVPAERREKLKTSRDKLRK", "down_seq": "FTPDHVVYARSKTAVYKVPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "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": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ], "site_lbl": "Ser300" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.302.302", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6NZI2-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6NZI2-1.314.314", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis.", "journal": "Analytical chemistry", "date": "2008", "authors": "Wang B, Malik R, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages.", "journal": "Journal of proteome research", "date": "2009", "authors": "Malik R, Lenobel R, Santamaria A, Ries A, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VPAERREKLKTSRDKLRKSF", "down_seq": "PDHVVYARSKTAVYKVPPFT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ], "site_lbl": "Thr302" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q6NZI2-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6NZI2-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6NZI2-1.314.314", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005", "authors": "Zhang Y, Wolf-Yadlin A, Ross PL, Pappin DJ, Rush J, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "15951569", "url": "https://glygen.org/publication/PubMed/15951569" } ] }, { "title": "Effects of HER2 overexpression on cell signaling networks governing proliferation and migration.", "journal": "Molecular systems biology", "date": "2006", "authors": "Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova V, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" } ] }, { "title": "Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.", "journal": "Journal of proteome research", "date": "2008", "authors": "Tsai CF, Wang YT, Chen YR, Lai CY, Lin PY, Pan KT, Chen JY, Khoo KH, Chen YJ", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15951569", "url": "https://glygen.org/publication/PubMed/15951569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EKLKTSRDKLRKSFTPDHVV", "down_seq": "ARSKTAVYKVPPFTFHVKKI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "15951569", "url": "https://glygen.org/publication/PubMed/15951569" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" }, { "database": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ], "site_lbl": "Tyr308" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6NZI2-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6NZI2-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6NZI2-1.302.302", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6NZI2-1.314.314", "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": "Q6NZI2-1.365.365", "start_pos": 365, "end_pos": 365, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "Vectorial proteomics reveal targeting, phosphorylation and specific fragmentation of polymerase I and transcript release factor (PTRF) at the surface of caveolae in human adipocytes.", "journal": "The Biochemical journal", "date": "2004", "authors": "Aboulaich N, Vainonen JP, Stralfors P, Vener AV", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "RefSeq", "id": "NP_036364", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_036364" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GADDDEGGAERGEAGDLRRG", "down_seq": "SPDVHALLEITEESDAVLVD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser365" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6NZI2-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6NZI2-1.376.376", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6NZI2-1.379.379", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.366.366", "start_pos": 366, "end_pos": 366, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Vectorial proteomics reveal targeting, phosphorylation and specific fragmentation of polymerase I and transcript release factor (PTRF) at the surface of caveolae in human adipocytes.", "journal": "The Biochemical journal", "date": "2004", "authors": "Aboulaich N, Vainonen JP, Stralfors P, Vener AV", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "RefSeq", "id": "NP_036364", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_036364" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ADDDEGGAERGEAGDLRRGS", "down_seq": "PDVHALLEITEESDAVLVDK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser366" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6NZI2-1.365.365", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6NZI2-1.376.376", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6NZI2-1.379.379", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6NZI2-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Vectorial proteomics reveal targeting, phosphorylation and specific fragmentation of polymerase I and transcript release factor (PTRF) at the surface of caveolae in human adipocytes.", "journal": "The Biochemical journal", "date": "2004", "authors": "Aboulaich N, Vainonen JP, Stralfors P, Vener AV", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "RefSeq", "id": "NP_036364", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_036364" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YPDAEAPEPSSAGAQAAEEP", "down_seq": "GAGSEELIKSDQVNGVLVLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "site_lbl": "Ser36" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q6NZI2-1.40.40", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6NZI2-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6NZI2-1.46.46", "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": "Q6NZI2-1.376.376", "start_pos": 376, "end_pos": 376, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GEAGDLRRGSSPDVHALLEI", "down_seq": "EESDAVLVDKSDSD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr376" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6NZI2-1.365.365", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6NZI2-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6NZI2-1.379.379", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6NZI2-1.387.387", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6NZI2-1.389.389", "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": "Q6NZI2-1.379.379", "start_pos": 379, "end_pos": 379, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "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": "GDLRRGSSPDVHALLEITEE", "down_seq": "DAVLVDKSDSD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser379" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6NZI2-1.365.365", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6NZI2-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6NZI2-1.376.376", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6NZI2-1.387.387", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6NZI2-1.389.389", "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": "Q6NZI2-1.387.387", "start_pos": 387, "end_pos": 387, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PDVHALLEITEESDAVLVDK", "down_seq": "DSD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser387" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6NZI2-1.376.376", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6NZI2-1.379.379", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6NZI2-1.389.389", "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": "Q6NZI2-1.389.389", "start_pos": 389, "end_pos": 389, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VHALLEITEESDAVLVDKSD", "down_seq": "", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser389" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6NZI2-1.376.376", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6NZI2-1.379.379", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.387.387", "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": "Q6NZI2-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Vectorial proteomics reveal targeting, phosphorylation and specific fragmentation of polymerase I and transcript release factor (PTRF) at the surface of caveolae in human adipocytes.", "journal": "The Biochemical journal", "date": "2004", "authors": "Aboulaich N, Vainonen JP, Stralfors P, Vener AV", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "RefSeq", "id": "NP_036364", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_036364" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "reference": [ { "type": "PubMed", "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAPEPSSAGAQAAEEPSGAG", "down_seq": "EELIKSDQVNGVLVLSLLDK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "PubMed", "id": "15242332", "url": "https://glygen.org/publication/PubMed/15242332" }, { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" } ], "site_lbl": "Ser40" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q6NZI2-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6NZI2-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6NZI2-1.46.46", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6NZI2-1.60.60", "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": "Q6NZI2-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SAGAQAAEEPSGAGSEELIK", "down_seq": "DQVNGVLVLSLLDKIIGAVD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "site_lbl": "Ser46" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6NZI2-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6NZI2-1.40.40", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6NZI2-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6NZI2-1.60.60", "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": "Q6NZI2-1.7.7", "start_pos": 7, "end_pos": 7, "uniprot_canonical_ac": "Q6NZI2-1", "length": 390, "uniprot_id": "CAVN1_HUMAN", "protein_name": "Caveolae-associated protein 1", "refseq_ac": "NP_036364", "refseq_name": "caveolae-associated protein 1 isoform 1", "gene_name": "CAVIN1", "gene_names_uniprotkb": "CAVIN1; FKSG13; PTRF", "gene_names_refseq": "CAVIN1; CAVIN; CGL4; FKSG13; PTRF; cavin-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" } ], "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": "UniProtKB", "id": "Q6NZI2", "url": "https://www.uniprot.org/uniprotkb/Q6NZI2" }, { "database": "iPTMnet", "id": "Q6NZI2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MEDPTL", "down_seq": "IVERPLPGYPDAEAPEPSSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6NZI2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6NZI2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Tyr7" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "244", "end_pos": "244" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "60", "end_pos": "60" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "7", "end_pos": "7" } ] } ], "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": "Q6P9F0-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "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": "Q6P9F0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6P9F0" }, { "database": "O-GlcNAc Atlas", "id": "Q6P9F0", "url": "https://oglcnac.org/atlas/detail/Q6P9F0" } ], "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": "Q6P9F0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6P9F0", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "Q6P9F0", "url": "https://oglcnac.org/atlas/detail/Q6P9F0", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2135559741", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2135559741", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2135559741", "url": "https://www.ensembl.org/id/rs2135559741", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KQQIDTVFGEKSVITLSSIF", "down_seq": "KDLVEKHNLPWSLGGKTQIE", "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": "Thr400", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6P9F0", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6P9F0" }, { "id": "Q6P9F0", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6P9F0" } ] } ], "snv": [ { "evidence": [ { "id": "rs2135559741", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2135559741" }, { "id": "rs2135559741", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2135559741" } ], "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": "12", "chr_pos": "122801344", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T400", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q6P9F0-1.391.391", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6P9F0-1.410.410", "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": "Q6P9F0-1.637.638", "start_pos": 637, "end_pos": 638, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ERAP75 functions as a coactivator to enhance estrogen receptor alpha transactivation in prostate stromal cells.", "journal": "The Prostate", "date": "2008", "authors": "Chen M, Ni J, Zhang Y, Muyan M, Yeh S", "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" }, { "database": "RefSeq", "id": "NP_958843", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_958843" } ], "reference": [ { "type": "PubMed", "id": "18563714", "url": "https://glygen.org/publication/PubMed/18563714" } ] }, { "title": "CCDC62/ERAP75 functions as a coactivator to enhance estrogen receptor beta-mediated transactivation and target gene expression in prostate cancer cells.", "journal": "Carcinogenesis", "date": "2009", "authors": "Chen M, Ni J, Chang HC, Lin CY, Muyan M, Yeh S", "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" }, { "database": "RefSeq", "id": "NP_958843", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_958843" } ], "reference": [ { "type": "PubMed", "id": "19126643", "url": "https://glygen.org/publication/PubMed/19126643" } ] } ], "crossref": [ { "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18563714", "url": "https://glygen.org/publication/PubMed/18563714", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19126643", "url": "https://glygen.org/publication/PubMed/19126643", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "LL", "start_aa": "L", "up_seq": "KASIVLPSQDDFSPTSKLQR", "down_seq": "AESRQMVTDLELSTLLPISH", "mutagenesis": [ { "sequence_org": "LL", "sequence_mut": "AA", "comment": "Abrogates interaction with ESR1 and ESR2.", "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" }, { "database": "PubMed", "id": "18563714", "url": "https://glygen.org/publication/PubMed/18563714" }, { "database": "PubMed", "id": "19126643", "url": "https://glygen.org/publication/PubMed/19126643" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6P9F0-1.629.629", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6P9F0-1.653.654", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6P9F0-1.653.654", "start_pos": 653, "end_pos": 654, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ERAP75 functions as a coactivator to enhance estrogen receptor alpha transactivation in prostate stromal cells.", "journal": "The Prostate", "date": "2008", "authors": "Chen M, Ni J, Zhang Y, Muyan M, Yeh S", "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" }, { "database": "RefSeq", "id": "NP_958843", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_958843" } ], "reference": [ { "type": "PubMed", "id": "18563714", "url": "https://glygen.org/publication/PubMed/18563714" } ] }, { "title": "CCDC62/ERAP75 functions as a coactivator to enhance estrogen receptor beta-mediated transactivation and target gene expression in prostate cancer cells.", "journal": "Carcinogenesis", "date": "2009", "authors": "Chen M, Ni J, Chang HC, Lin CY, Muyan M, Yeh S", "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" }, { "database": "RefSeq", "id": "NP_958843", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_958843" } ], "reference": [ { "type": "PubMed", "id": "19126643", "url": "https://glygen.org/publication/PubMed/19126643" } ] } ], "crossref": [ { "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18563714", "url": "https://glygen.org/publication/PubMed/18563714", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19126643", "url": "https://glygen.org/publication/PubMed/19126643", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "LL", "start_aa": "L", "up_seq": "KLQRLLAESRQMVTDLELST", "down_seq": "PISHENLTGSATNKSEVPEE", "mutagenesis": [ { "sequence_org": "LL", "sequence_mut": "AA", "comment": "No effect on interaction with ESR1 or ESR2.", "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" }, { "database": "PubMed", "id": "18563714", "url": "https://glygen.org/publication/PubMed/18563714" }, { "database": "PubMed", "id": "19126643", "url": "https://glygen.org/publication/PubMed/19126643" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6P9F0-1.637.638", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6P9F0-1.662.662", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6P9F0-1.664.664", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6P9F0-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EAVNHIADCSGKFKMLEHAL", "down_seq": "DAKMAETCIVKEKQDYKQKL", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "12", "chr_pos": "122788833", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R192", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "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": "Q6P9F0-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LKEDLNEKTTENNEQREEII", "down_seq": "LKQEKSCLHDELLFTVEREK", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" } ], "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 (4).", "chr_id": "12", "chr_pos": "122792073", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R242", "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: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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "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": "Q6P9F0-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs146255239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146255239", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs146255239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146255239", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs146255239", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146255239#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs146255239", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146255239", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HDELLFTVEREKRKDELLNI", "down_seq": "KSKQERTNSELHNLRQIYVK", "snv": [ { "evidence": [ { "id": "rs146255239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146255239" }, { "id": "rs146255239", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146255239" }, { "id": "rs146255239", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146255239#frequency_tab" }, { "id": "rs146255239", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146255239" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIA->NIS).", "chr_id": "12", "chr_pos": "122797345", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A271", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs146255239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146255239" }, { "id": "rs146255239", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146255239" }, { "id": "rs146255239", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146255239#frequency_tab" }, { "id": "rs146255239", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146255239" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIA->NIT).", "chr_id": "12", "chr_pos": "122797345", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A271", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "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": "Q6P9F0-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779139526", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779139526", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779139526", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779139526", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779139526", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779139526#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779139526", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779139526", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LHNLRQIYVKQQSDLQFLNF", "down_seq": "VENSQELIQMYDSKMEESKA", "snv": [ { "evidence": [ { "id": "rs779139526", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779139526" }, { "id": "rs779139526", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779139526" }, { "id": "rs779139526", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779139526#frequency_tab" }, { "id": "rs779139526", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779139526" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFN->NFS).", "chr_id": "12", "chr_pos": "122798128", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N302", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "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": "Q6P9F0-1.339.339", "start_pos": 339, "end_pos": 339, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs373036488", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373036488", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373036488", "url": "https://www.ensembl.org/id/rs373036488", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs373036488", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373036488", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ESKALDSSRDMCLSDLENNH", "down_seq": "KVDIKREKNQKSLFKDQKFE", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" }, { "id": "rs373036488", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373036488" }, { "id": "rs373036488", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs373036488" }, { "id": "rs373036488", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373036488" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NHP->NHS).", "chr_id": "12", "chr_pos": "122801161", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P339", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "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": "Q6P9F0-1.374.374", "start_pos": 374, "end_pos": 374, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs774474363", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774474363", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774474363", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774474363", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774474363", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774474363#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774474363", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774474363", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs774474363", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774474363", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KDQKFEAMLVQQNRSDKSSC", "down_seq": "ECKEKKQQIDTVFGEKSVIT", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" }, { "id": "rs774474363", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774474363" }, { "id": "rs774474363", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774474363" }, { "id": "rs774474363", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774474363#frequency_tab" }, { "id": "rs774474363", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774474363" }, { "id": "rs774474363", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774474363" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DEC->NEC).", "chr_id": "12", "chr_pos": "122801266", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D374", "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: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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q6P9F0-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6P9F0-1.391.391", "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": "Q6P9F0-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "FEAMLVQQNRSDKSSCDECK", "down_seq": "KKQQIDTVFGEKSVITLSSI", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "122801280", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E378", "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: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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q6P9F0-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6P9F0-1.391.391", "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": "Q6P9F0-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ISTIEKQRKELQLLIGELKD", "down_seq": "DKELNDMVAVHQQQLLSWEE", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "122777572", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R40", "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: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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "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": "Q6P9F0-1.410.410", "start_pos": 410, "end_pos": 410, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2135559835", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2135559835", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2135559835", "url": "https://www.ensembl.org/id/rs2135559835", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2135559835", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2135559835", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KSVITLSSIFTKDLVEKHNL", "down_seq": "WSLGGKTQIEPENKITLCKI", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" }, { "id": "rs2135559835", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2135559835" }, { "id": "rs2135559835", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2135559835" }, { "id": "rs2135559835", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2135559835" } ], "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 (NLP->NLS).", "chr_id": "12", "chr_pos": "122801374", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P410", "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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6P9F0-1.391.391", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6P9F0-1.400.400", "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": "Q6P9F0-1.463.463", "start_pos": 463, "end_pos": 463, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772372235", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772372235", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772372235", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772372235", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772372235", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772372235#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772372235", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772372235", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QNEGKQPSETPTLSDEKQWH", "down_seq": "VSVYLGLTNCPSSKHPEKLD", "snv": [ { "evidence": [ { "id": "rs772372235", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772372235" }, { "id": "rs772372235", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772372235" }, { "id": "rs772372235", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772372235#frequency_tab" }, { "id": "rs772372235", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772372235" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DVS->NVS).", "chr_id": "12", "chr_pos": "122801533", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D463", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q6P9F0-1.474.474", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1194993713", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194993713", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1194993713", "url": "https://www.ensembl.org/id/rs1194993713", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TLSDEKQWHDVSVYLGLTNC", "down_seq": "SSKHPEKLDVECQDQMERSE", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" }, { "id": "rs1194993713", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194993713" }, { "id": "rs1194993713", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1194993713" } ], "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 (NCP->NCS).", "chr_id": "12", "chr_pos": "122801566", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P474", "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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6P9F0-1.463.463", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.503.503", "start_pos": 503, "end_pos": 503, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2031317137", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2031317137", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2031317137", "url": "https://www.ensembl.org/id/rs2031317137", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DVECQDQMERSEISCCQKNE", "down_seq": "CLGESGMCDSKCCHPSNFII", "snv": [ { "evidence": [ { "id": "rs2031317137", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2031317137" }, { "id": "rs2031317137", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2031317137" } ], "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": "12", "chr_pos": "122801653", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A503", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q6P9F0-1.522.522", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.522.522", "start_pos": 522, "end_pos": 522, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs370139805", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370139805", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370139805", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370139805", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EACLGESGMCDSKCCHPSNF", "down_seq": "IEAPGHMSDVEWMSIFKPSK", "snv": [ { "evidence": [ { "id": "rs370139805", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370139805" }, { "id": "rs370139805", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370139805" } ], "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": "12", "chr_pos": "122801711", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I522", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6P9F0-1.503.503", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.554.554", "start_pos": 554, "end_pos": 554, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs764145983", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764145983", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764145983", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764145983", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764145983", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764145983#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764145983", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764145983", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764145983", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764145983", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "WMSIFKPSKMQRIVRLKSGC", "down_seq": "CSESICGTQHDSPASELIAI", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" }, { "id": "rs764145983", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764145983" }, { "id": "rs764145983", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764145983" }, { "id": "rs764145983", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764145983#frequency_tab" }, { "id": "rs764145983", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764145983" }, { "id": "rs764145983", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764145983" } ], "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 (TCS->NCS).", "chr_id": "12", "chr_pos": "122801807", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T554", "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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "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": "Q6P9F0-1.599.599", "start_pos": 599, "end_pos": 599, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1593815596", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1593815596", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1593815596", "url": "https://www.ensembl.org/id/rs1593815596", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1593815596", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1593815596", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SLGSSKSALREDETESSSNK", "down_seq": "NSPTSLLIYKDAPAFNEKAS", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" }, { "id": "rs1593815596", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1593815596" }, { "id": "rs1593815596", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1593815596" }, { "id": "rs1593815596", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1593815596" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KNS->NNS).", "chr_id": "12", "chr_pos": "122806241", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K599", "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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q6P9F0-1.606.606", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.606.606", "start_pos": 606, "end_pos": 606, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "ALREDETESSSNKKNSPTSL", "down_seq": "IYKDAPAFNEKASIVLPSQD", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "122806260", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L606", "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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6P9F0-1.599.599", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.629.629", "start_pos": 629, "end_pos": 629, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KDAPAFNEKASIVLPSQDDF", "down_seq": "PTSKLQRLLAESRQMVTDLE", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" } ], "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 (3).", "chr_id": "12", "chr_pos": "122813304", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S629", "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": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q6P9F0-1.637.638", "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": "Q6P9F0-1.662.662", "start_pos": 662, "end_pos": 662, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RQMVTDLELSTLLPISHENL", "down_seq": "GSATNKSEVPEESAQKNTFV", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TGS->NGS).", "chr_id": "12", "chr_pos": "122813403", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T662", "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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6P9F0-1.653.654", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6P9F0-1.664.664", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6P9F0-1.681.681", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.664.664", "start_pos": 664, "end_pos": 664, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P9F0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MVTDLELSTLLPISHENLTG", "down_seq": "ATNKSEVPEESAQKNTFVSY", "snv": [ { "evidence": [ { "id": "Q6P9F0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P9F0" } ], "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 (SAT->NAT).", "chr_id": "12", "chr_pos": "122813409", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S664", "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": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6P9F0-1.653.654", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6P9F0-1.662.662", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6P9F0-1.681.681", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.681.681", "start_pos": 681, "end_pos": 681, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1163020754", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1163020754", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1163020754", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1163020754#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1163020754", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1163020754", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "LTGSATNKSEVPEESAQKNT", "down_seq": "VSY", "snv": [ { "evidence": [ { "id": "rs1163020754", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1163020754" }, { "id": "rs1163020754", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1163020754#frequency_tab" }, { "id": "rs1163020754", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1163020754" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTF->NTC).", "chr_id": "12", "chr_pos": "122823406", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F681", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6P9F0-1.662.662", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q6P9F0-1.664.664", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P9F0-1.391.391", "start_pos": 391, "end_pos": 391, "uniprot_canonical_ac": "Q6P9F0-1", "length": 684, "uniprot_id": "CCD62_HUMAN", "protein_name": "Coiled-coil domain-containing protein 62", "refseq_ac": "NP_958843", "refseq_name": "coiled-coil domain-containing protein 62", "gene_name": "CCDC62", "gene_names_uniprotkb": "CCDC62", "gene_names_refseq": "CCDC62; CT109; ERAP75; SPGF67; TSP-NY", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P9F0", "url": "https://www.uniprot.org/uniprotkb/Q6P9F0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q6P9F0-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6P9F0-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] } ], "crossref": [ { "id": "Q6P9F0", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6P9F0", "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": "SSCDECKEKKQQIDTVFGEK", "down_seq": "VITLSSIFTKDLVEKHNLPW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6P9F0", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6P9F0" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ], "site_lbl": "Ser391" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "400", "end_pos": "400" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "637", "end_pos": "638" }, { "start_pos": "653", "end_pos": "654" } ] }, { "type": "snv", "site_list": [ { "start_pos": "192", "end_pos": "192" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "554", "end_pos": "554" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "681", "end_pos": "681" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "391", "end_pos": "391" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6P9F0-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6P9F0-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6P9F0-1.400.400", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6P9F0-1.410.410", "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": "Q6ZN84-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "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": "Q6ZN84", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN84" }, { "database": "O-GlcNAc Atlas", "id": "Q6ZN84", "url": "https://oglcnac.org/atlas/detail/Q6ZN84" } ], "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": "Q6ZN84", "url": "https://oglcnac.org/atlas/detail/Q6ZN84", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RERKCKLKDQSDKEEGTRDI", "down_seq": "SPKRLRDRQALFPAKVTNVS", "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": "Ser255", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q6ZN84", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6ZN84" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6ZN84-1.256.256", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6ZN84-1.275.275", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZN84-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "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": "Q6ZN84", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN84" }, { "database": "O-GlcNAc Atlas", "id": "Q6ZN84", "url": "https://oglcnac.org/atlas/detail/Q6ZN84" } ], "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": "Q6ZN84", "url": "https://oglcnac.org/atlas/detail/Q6ZN84", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ERKCKLKDQSDKEEGTRDIS", "down_seq": "PKRLRDRQALFPAKVTNVSL", "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": "Ser256", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q6ZN84", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6ZN84" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6ZN84-1.255.255", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6ZN84-1.275.275", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZN84-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "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": "Q6ZN84", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN84" }, { "database": "O-GlcNAc Atlas", "id": "Q6ZN84", "url": "https://oglcnac.org/atlas/detail/Q6ZN84" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Comparative analysis of Cu (I)-catalyzed alkyne-azide cycloaddition (CuAAC) and strain-promoted alkyne-azide cycloaddition (SPAAC) in O-GlcNAc proteomics.", "journal": "Electrophoresis", "date": "2016", "authors": "Li S, Zhu H, Wang J, Wang X, Li X, Ma C, Wen L, Yu B, Wang Y, Li J, Wang PG", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZN84", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN84" } ], "reference": [ { "type": "PubMed", "id": "26853435", "url": "https://glygen.org/publication/PubMed/26853435" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZN84", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN84", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "26853435", "url": "https://glygen.org/publication/PubMed/26853435", "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": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q6ZN84", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN84" }, { "id": "26853435", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26853435" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "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": "Q6ZN84-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LDTIARALQDLGRQVLPTLP", "down_seq": "LSQEEVSIIWGNVSEFVRRQ", "snv": [ { "evidence": [ { "id": "Q6ZN84", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "11", "chr_pos": "86375228", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S22", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "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": "Q6ZN84-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1176721699", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1176721699", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1176721699", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1176721699#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1176721699", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1176721699", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LKHDSEMKPQTSPACQDHNK", "down_seq": "GQEMCYVCLQRAQRNSLLYY", "snv": [ { "evidence": [ { "id": "rs1176721699", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1176721699" }, { "id": "rs1176721699", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1176721699#frequency_tab" }, { "id": "rs1176721699", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1176721699" } ], "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": "11", "chr_pos": "86407693", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A321", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "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": "Q6ZN84-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "QKNAAYNLGVAEAIRNHKNE", "down_seq": "PEFYKSFLFDKRPLSPALNA", "snv": [ { "evidence": [ { "id": "Q6ZN84", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NEK->NET).", "chr_id": "11", "chr_pos": "86409352", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K402", "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": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q6ZN84-1.408.408", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6ZN84-1.417.417", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6ZN84-1.419.419", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZN84-1.408.408", "start_pos": 408, "end_pos": 408, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NLGVAEAIRNHKNEKPEFYK", "down_seq": "FLFDKRPLSPALNALKQEEY", "snv": [ { "evidence": [ { "id": "Q6ZN84", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84" } ], "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: num. of cancers (3).", "chr_id": "11", "chr_pos": "86412391", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S408", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6ZN84-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6ZN84-1.417.417", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6ZN84-1.419.419", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZN84-1.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KNEKPEFYKSFLFDKRPLSP", "down_seq": "LNALKQEEYSRSLLKQMDNR", "snv": [ { "evidence": [ { "id": "Q6ZN84", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84" } ], "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": "11", "chr_pos": "86412424", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A419", "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": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6ZN84-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6ZN84-1.408.408", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6ZN84-1.417.417", "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": "Q6ZN84-1.444.444", "start_pos": 444, "end_pos": 444, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762028031", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762028031", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762028031", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762028031", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762028031", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762028031#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762028031", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762028031", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KQEEYSRSLLKQMDNRQENE", "down_seq": "KQRQYRELMDRLEQVQLTEE", "snv": [ { "evidence": [ { "id": "rs762028031", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762028031" }, { "id": "rs762028031", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762028031" }, { "id": "rs762028031", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762028031#frequency_tab" }, { "id": "rs762028031", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762028031" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEI->NET).", "chr_id": "11", "chr_pos": "86412499", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I444", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "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": "Q6ZN84-1.495.495", "start_pos": 495, "end_pos": 495, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs150696307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150696307", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150696307", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150696307", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs150696307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150696307", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150696307", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150696307#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150696307", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150696307", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DKMEETQCYKRALDAQIKNK", "down_seq": "SRLPPFEPDSSEPIFGKNEG", "snv": [ { "evidence": [ { "id": "rs150696307", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150696307" }, { "id": "rs150696307", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150696307" }, { "id": "rs150696307", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150696307" }, { "id": "rs150696307", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150696307#frequency_tab" }, { "id": "rs150696307", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150696307" } ], "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": "11", "chr_pos": "86415105", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.00372841", "site_lbl": "P495", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs150696307", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150696307" }, { "id": "rs150696307", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150696307" }, { "id": "rs150696307", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150696307" }, { "id": "rs150696307", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150696307#frequency_tab" }, { "id": "rs150696307", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150696307" } ], "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": "11", "chr_pos": "86415105", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.00372841", "site_lbl": "P495", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q6ZN84-1.515.515", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q6ZN84-1.515.515", "start_pos": 515, "end_pos": 515, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760418118", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760418118", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760418118", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760418118", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760418118", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760418118", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PSRLPPFEPDSSEPIFGKNE", "down_seq": "ELMVEKQKREQNYMKHQLEA", "snv": [ { "evidence": [ { "id": "rs760418118", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760418118" }, { "id": "rs760418118", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760418118" }, { "id": "rs760418118", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760418118" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEG->NES).", "chr_id": "11", "chr_pos": "86415165", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G515", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6ZN84-1.495.495", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6ZN84-1.529.529", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZN84-1.529.529", "start_pos": 529, "end_pos": 529, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773477496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773477496", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773477496", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773477496#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773477496", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773477496", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "IFGKNEGELMVEKQKREQNY", "down_seq": "KHQLEAAANHKRKAILHQLV", "snv": [ { "evidence": [ { "id": "rs773477496", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773477496" }, { "id": "rs773477496", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773477496#frequency_tab" }, { "id": "rs773477496", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773477496" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYM->NYT).", "chr_id": "11", "chr_pos": "86415208", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M529", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6ZN84-1.515.515", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZN84-1.606.606", "start_pos": 606, "end_pos": 606, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DWERSAAMKKQRDLEDKAFE", "down_seq": "ASDKLFLLDQCEKYRRCKQC", "snv": [ { "evidence": [ { "id": "Q6ZN84", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84" } ], "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": "11", "chr_pos": "86420052", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R606", "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" } ] }, { "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": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q6ZN84-1.624.624", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZN84-1.624.624", "start_pos": 624, "end_pos": 624, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs142078674", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142078674", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142078674", "url": "https://www.ensembl.org/id/rs142078674", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FERASDKLFLLDQCEKYRRC", "down_seq": "QCQRRTSNVGESNLWPLNKF", "snv": [ { "evidence": [ { "id": "rs142078674", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142078674" }, { "id": "rs142078674", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs142078674" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KQC->NQC).", "chr_id": "11", "chr_pos": "86422628", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K624", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6ZN84-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6ZN84-1.629.629", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6ZN84-1.639.639", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZN84-1.629.629", "start_pos": 629, "end_pos": 629, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DKLFLLDQCEKYRRCKQCQR", "down_seq": "TSNVGESNLWPLNKFLPGSR", "snv": [ { "evidence": [ { "id": "Q6ZN84", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84" } ], "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": "11", "chr_pos": "86422641", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R629", "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" ] }, { "evidence": [ { "id": "Q6ZN84", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84" } ], "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": "11", "chr_pos": "86422642", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R629", "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: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": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q6ZN84-1.624.624", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6ZN84-1.639.639", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q6ZN84-1.639.639", "start_pos": 639, "end_pos": 639, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "KYRRCKQCQRRTSNVGESNL", "down_seq": "PLNKFLPGSRLLV", "snv": [ { "evidence": [ { "id": "Q6ZN84", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN84" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLW->NLC).", "chr_id": "11", "chr_pos": "86422673", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "W639", "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": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6ZN84-1.624.624", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6ZN84-1.629.629", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZN84-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RPGTVDSVLSSREALRKWPS", "down_seq": "VLAFPRIELKEMENKLPMET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "site_lbl": "Ser206" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "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": "Q6ZN84-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSPKRLRDRQALFPAKVTNV", "down_seq": "LLEKFERSESGGKIMTPESL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "site_lbl": "Ser275" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6ZN84-1.255.255", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q6ZN84-1.256.256", "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": "Q6ZN84-1.296.296", "start_pos": 296, "end_pos": 296, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLEKFERSESGGKIMTPESL", "down_seq": "YPSCLKHDSEMKPQTSPACQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "site_lbl": "Ser296" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "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": "Q6ZN84-1.417.417", "start_pos": 417, "end_pos": 417, "uniprot_canonical_ac": "Q6ZN84-1", "length": 652, "uniprot_id": "CCD81_HUMAN", "protein_name": "Coiled-coil domain-containing protein 81", "refseq_ac": "NP_001149946", "refseq_name": "coiled-coil domain-containing protein 81 isoform 1", "gene_name": "CCDC81", "gene_names_uniprotkb": "CCDC81", "gene_names_refseq": "CCDC81", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NHKNEKPEFYKSFLFDKRPL", "down_seq": "PALNALKQEEYSRSLLKQMD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN84", "url": "https://www.uniprot.org/uniprotkb/Q6ZN84" } ], "site_lbl": "Ser417" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" } ] }, { "type": "snv", "site_list": [ { "start_pos": "22", "end_pos": "22" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "629", "end_pos": "629" }, { "start_pos": "639", "end_pos": "639" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "417", "end_pos": "417" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6ZN84-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6ZN84-1.408.408", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6ZN84-1.419.419", "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": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZSJ8-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q6ZSJ8-1", "length": 110, "uniprot_id": "CA122_HUMAN", "protein_name": "Uncharacterized protein C1orf122", "refseq_ac": "NP_001136198", "refseq_name": "uncharacterized protein C1orf122 isoform 2", "gene_name": "C1orf122", "gene_names_uniprotkb": "C1orf122", "gene_names_refseq": "ALAESM; C1orf122", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZSJ8", "url": "https://www.uniprot.org/uniprotkb/Q6ZSJ8" } ], "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": "Q6ZSJ8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZSJ8" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZSJ8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZSJ8", "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": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q6ZSJ8", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZSJ8" } ] } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "82", "end_pos": "82" } ] } ], "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": "Q6ZSJ8-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "Q6ZSJ8-1", "length": 110, "uniprot_id": "CA122_HUMAN", "protein_name": "Uncharacterized protein C1orf122", "refseq_ac": "NP_001136198", "refseq_name": "uncharacterized protein C1orf122 isoform 2", "gene_name": "C1orf122", "gene_names_uniprotkb": "C1orf122", "gene_names_refseq": "ALAESM; C1orf122", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZSJ8", "url": "https://www.uniprot.org/uniprotkb/Q6ZSJ8" } ], "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": "Q6ZSJ8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZSJ8-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6ZSJ8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZSJ8", "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": "EEMLRQLGRRRPEPAGGGNV", "down_seq": "AKPGAPPQPAVSARGGFPKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6ZSJ8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZSJ8" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser82" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "82", "end_pos": "82" } ] } ], "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": "Q7Z5W3-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SLPDGETCSDASREFRLLCC", "down_seq": "IDPVLVKRAEKECPFPDALT", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q7Z5W3-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5W3-1.118.118", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5W3-1.120.120", "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": "Q7Z5W3-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LPDGETCSDASREFRLLCCD", "down_seq": "DPVLVKRAEKECPFPDALTF", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "G", "comment": "Decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q7Z5W3-1.110.110", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5W3-1.118.118", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q7Z5W3-1.120.120", "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": "Q7Z5W3-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SDASREFRLLCCDIDPVLVK", "down_seq": "AEKECPFPDALTFITLDFMN", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Slightly decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q7Z5W3-1.110.110", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5W3-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5W3-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7Z5W3-1.135.135", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q7Z5W3-1.136.136", "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": "Q7Z5W3-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LVKRAEKECPFPDALTFITL", "down_seq": "FMNQRTRKVLLSSFLSQFGR", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q7Z5W3-1.118.118", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q7Z5W3-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5W3-1.136.136", "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": "Q7Z5W3-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "VKRAEKECPFPDALTFITLD", "down_seq": "MNQRTRKVLLSSFLSQFGRS", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "G", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q7Z5W3-1.118.118", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q7Z5W3-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5W3-1.135.135", "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": "Q7Z5W3-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLSSFLSQFGRSVFDIGFCM", "down_seq": "ITMWIHLNHGDHGLWEFLAH", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q7Z5W3-1.166.166", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5W3-1.169.169", "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": "Q7Z5W3-1.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LSSFLSQFGRSVFDIGFCMS", "down_seq": "TMWIHLNHGDHGLWEFLAHL", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "G", "comment": "Decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q7Z5W3-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5W3-1.169.169", "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": "Q7Z5W3-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "FLSQFGRSVFDIGFCMSITM", "down_seq": "IHLNHGDHGLWEFLAHLSSL", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "F", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q7Z5W3-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5W3-1.166.166", "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": "Q7Z5W3-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "GLWEFLAHLSSLCHYLLVEP", "down_seq": "PWKCYRAAARRLRKLGLHDF", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q7Z5W3-1.211.212", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "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": "Q7Z5W3-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EFLAHLSSLCHYLLVEPQPW", "down_seq": "CYRAAARRLRKLGLHDFDHF", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5W3-1.211.212", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "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": "Q7Z5W3-1.201.204", "start_pos": 201, "end_pos": 204, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "KCYR", "start_aa": "K", "up_seq": "EFLAHLSSLCHYLLVEPQPW", "down_seq": "AAARRLRKLGLHDFDHFHSL", "mutagenesis": [ { "sequence_org": "KCYR", "sequence_mut": "ACYA", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5W3-1.211.212", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "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": "Q7Z5W3-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AHLSSLCHYLLVEPQPWKCY", "down_seq": "AAARRLRKLGLHDFDHFHSL", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5W3-1.211.212", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "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": "Q7Z5W3-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SLCHYLLVEPQPWKCYRAAA", "down_seq": "RLRKLGLHDFDHFHSLAIRG", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Strongly decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5W3-1.211.212", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "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": "Q7Z5W3-1.208.209", "start_pos": 208, "end_pos": 209, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "RR", "start_aa": "R", "up_seq": "SLCHYLLVEPQPWKCYRAAA", "down_seq": "LRKLGLHDFDHFHSLAIRGD", "mutagenesis": [ { "sequence_org": "RR", "sequence_mut": "AA", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5W3-1.211.212", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "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": "Q7Z5W3-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5W3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5W3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LCHYLLVEPQPWKCYRAAAR", "down_seq": "LRKLGLHDFDHFHSLAIRGD", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "snv": [ { "evidence": [ { "id": "Q7Z5W3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5W3" } ], "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 (3).", "chr_id": "12", "chr_pos": "49838625", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R209", "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": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5W3-1.211.212", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "Q7Z5W3-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HYLLVEPQPWKCYRAAARRL", "down_seq": "KLGLHDFDHFHSLAIRGDMP", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q7Z5W3-1.211.212", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "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": "Q7Z5W3-1.211.212", "start_pos": 211, "end_pos": 212, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "RK", "start_aa": "R", "up_seq": "HYLLVEPQPWKCYRAAARRL", "down_seq": "LGLHDFDHFHSLAIRGDMPN", "mutagenesis": [ { "sequence_org": "RK", "sequence_mut": "AA", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q7Z5W3-1.212.212", "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": "Q7Z5W3-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "YLLVEPQPWKCYRAAARRLR", "down_seq": "LGLHDFDHFHSLAIRGDMPN", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Decreased O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q7Z5W3-1.198.198", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q7Z5W3-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q7Z5W3-1.201.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q7Z5W3-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5W3-1.208.208", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5W3-1.208.209", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5W3-1.209.209", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5W3-1.211.211", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q7Z5W3-1.211.212", "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": "Q7Z5W3-1.257.257", "start_pos": 257, "end_pos": 257, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ILTQDHGMELICCFGNTSWD", "down_seq": "SLLLFRAKQTIETHPIPESL", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "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": "Q7Z5W3-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AEEESRVLAPGAAPFGNFPH", "down_seq": "SRFHPPEQRLRLLPPELLRQ", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] }, { "sequence_org": "Y", "sequence_mut": "F", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q7Z5W3-1.46.46", "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": "Q7Z5W3-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PGAAPFGNFPHYSRFHPPEQ", "down_seq": "LRLLPPELLRQLFPESPENG", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q7Z5W3-1.37.37", "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": "Q7Z5W3-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PELLRQLFPESPENGPILGL", "down_seq": "VGCNSGDLSVALYKHFLSLP", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 0, "direction": "upstream", "id": "Q7Z5W3-1.72.74", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5W3-1.74.74", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5W3-1.76.76", "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": "Q7Z5W3-1.72.74", "start_pos": 72, "end_pos": 74, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human RNA methyltransferase BCDIN3D regulates microRNA processing.", "journal": "Cell", "date": "2012", "authors": "Xhemalce B, Robson SC, Kouzarides T", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "Reactome", "id": "R-HSA-203927", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-203927" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "23063121", "url": "https://glygen.org/publication/PubMed/23063121" } ] }, { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] }, { "title": "Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA.", "journal": "Nucleic acids research", "date": "2017", "authors": "Martinez A, Yamashita S, Nagaike T, Sakaguchi Y, Suzuki T, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "28119416", "url": "https://glygen.org/publication/PubMed/28119416" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23063121", "url": "https://glygen.org/publication/PubMed/23063121", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28119416", "url": "https://glygen.org/publication/PubMed/28119416", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DVG", "start_aa": "D", "up_seq": "PELLRQLFPESPENGPILGL", "down_seq": "CNSGDLSVALYKHFLSLPDG", "mutagenesis": [ { "sequence_org": "DVG", "sequence_mut": "AVA", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "23063121", "url": "https://glygen.org/publication/PubMed/23063121" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" }, { "database": "PubMed", "id": "28119416", "url": "https://glygen.org/publication/PubMed/28119416" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 0, "direction": "downstream", "id": "Q7Z5W3-1.72.72", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q7Z5W3-1.74.74", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5W3-1.76.76", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5W3-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LLRQLFPESPENGPILGLDV", "down_seq": "CNSGDLSVALYKHFLSLPDG", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q7Z5W3-1.72.72", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q7Z5W3-1.72.74", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5W3-1.76.76", "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": "Q7Z5W3-1.76.76", "start_pos": 76, "end_pos": 76, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.", "journal": "Nucleic acids research", "date": "2020", "authors": "Liu Y, Martinez A, Yamashita S, Tomita K", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "RefSeq", "id": "NP_859059", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_859059" } ], "reference": [ { "type": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "crossref": [ { "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RQLFPESPENGPILGLDVGC", "down_seq": "SGDLSVALYKHFLSLPDGET", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Abolished O-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" }, { "database": "PubMed", "id": "31919512", "url": "https://glygen.org/publication/PubMed/31919512" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q7Z5W3-1.72.72", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5W3-1.72.74", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5W3-1.74.74", "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": "Q7Z5W3-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "Q7Z5W3-1", "length": 292, "uniprot_id": "BN3D2_HUMAN", "protein_name": "RNA 5'-monophosphate methyltransferase", "refseq_ac": "NP_859059", "refseq_name": "RNA 5'-monophosphate methyltransferase", "gene_name": "BCDIN3D", "gene_names_uniprotkb": "BCDIN3D", "gene_names_refseq": "BCDIN3D", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z5W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z5W3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5W3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ASREFRLLCCDIDPVLVKRA", "down_seq": "KECPFPDALTFITLDFMNQR", "snv": [ { "evidence": [ { "id": "Q7Z5W3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5W3" } ], "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 (3).", "chr_id": "12", "chr_pos": "49838892", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E120", "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": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "201", "end_pos": "204" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "208", "end_pos": "209" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "211", "end_pos": "212" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "72", "end_pos": "74" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "snv", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "209", "end_pos": "209" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q7Z5W3-1.110.110", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q7Z5W3-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5W3-1.118.118", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q7Z5W3-1.135.135", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q7Z5W3-1.136.136", "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": "Q86Y33-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q86Y33", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86Y33" }, { "database": "O-GlcNAc Atlas", "id": "Q86Y33", "url": "https://oglcnac.org/atlas/detail/Q86Y33" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q86Y33", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86Y33" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Z-band alternatively spliced PDZ motif protein (ZASP) is the major O-linked beta-N-acetylglucosamine-substituted protein in human heart myofibrils.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Leung MC, Hitchen PG, Ward DG, Messer AE, Marston SB", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86Y33", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86Y33" } ], "reference": [ { "type": "PubMed", "id": "23271734", "url": "https://glygen.org/publication/PubMed/23271734" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86Y33", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86Y33", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23271734", "url": "https://glygen.org/publication/PubMed/23271734", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86Y33", "url": "https://oglcnac.org/atlas/detail/Q86Y33", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1743490188", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1743490188", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1743490188", "url": "https://www.ensembl.org/id/rs1743490188", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KSNFAKRLSAEVPVASSPIT", "down_seq": "RWQQSQTRALSSDSFGEEQS", "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": "Thr75", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q86Y33", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86Y33" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "23271734", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23271734" }, { "id": "Q86Y33", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q86Y33" } ] } ], "snv": [ { "evidence": [ { "id": "rs1743490188", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1743490188" }, { "id": "rs1743490188", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1743490188" } ], "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": "5", "chr_pos": "55146759", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T75", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q86Y33-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q86Y33-1.80.80", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86Y33-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1217479600", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1217479600", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1217479600", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1217479600#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1217479600", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1217479600", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LTLGSRKEQLKTPSKGISET", "down_seq": "NSALHFCKAPHAMDRDWKES", "snv": [ { "evidence": [ { "id": "rs1217479600", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1217479600" }, { "id": "rs1217479600", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1217479600#frequency_tab" }, { "id": "rs1217479600", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1217479600" } ], "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 (SNS->NNS).", "chr_id": "5", "chr_pos": "55143592", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S136", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q86Y33-1.141.141", "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": "Q86Y33-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86Y33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "RKEQLKTPSKGISETSNSAL", "down_seq": "FCKAPHAMDRDWKESVASKG", "snv": [ { "evidence": [ { "id": "Q86Y33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HFC->NFC).", "chr_id": "5", "chr_pos": "55143578", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H141", "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": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q86Y33-1.136.136", "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": "Q86Y33-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs149975868", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149975868", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149975868", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149975868#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs149975868", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149975868", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "INDSILQPEVKIHITGLRND", "down_seq": "YLNILDWSFQNLVAIALGSA", "snv": [ { "evidence": [ { "id": "rs149975868", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149975868" }, { "id": "rs149975868", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149975868#frequency_tab" }, { "id": "rs149975868", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149975868" } ], "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 (NDY->NDC).", "chr_id": "5", "chr_pos": "55133414", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y232", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "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": "Q86Y33-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1453953606", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1453953606", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1453953606", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1453953606#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1453953606", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1453953606", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QNLVAIALGSAVYIWNGENH", "down_seq": "GIENIDLSLTCNYISSVSWI", "snv": [ { "evidence": [ { "id": "rs1453953606", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1453953606" }, { "id": "rs1453953606", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1453953606#frequency_tab" }, { "id": "rs1453953606", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1453953606" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHN->NHS).", "chr_id": "5", "chr_pos": "55128530", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N262", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q86Y33-1.264.264", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86Y33-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1450238532", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1450238532", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1450238532", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1450238532#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LVAIALGSAVYIWNGENHNG", "down_seq": "ENIDLSLTCNYISSVSWIKE", "snv": [ { "evidence": [ { "id": "rs1450238532", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1450238532" }, { "id": "rs1450238532", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1450238532#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGI->NGT).", "chr_id": "5", "chr_pos": "55128524", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I264", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q86Y33-1.262.262", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86Y33-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86Y33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CLAVGTSEGEVQLWDVVTKK", "down_seq": "LRNMLGHLSVVGALSWNHFI", "snv": [ { "evidence": [ { "id": "Q86Y33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33" } ], "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": "5", "chr_pos": "55127326", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R307", "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: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": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q86Y33-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q86Y33-1.327.327", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86Y33-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86Y33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "EGEVQLWDVVTKKRLRNMLG", "down_seq": "LSVVGALSWNHFILSSGSRL", "snv": [ { "evidence": [ { "id": "Q86Y33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HLS->NLS).", "chr_id": "5", "chr_pos": "55127306", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H314", "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": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q86Y33-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q86Y33-1.327.327", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86Y33-1.327.327", "start_pos": 327, "end_pos": 327, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1341342207", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1341342207", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1341342207", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1341342207", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RLRNMLGHLSVVGALSWNHF", "down_seq": "LSSGSRLGRVYHHDVRVAQH", "snv": [ { "evidence": [ { "id": "rs1341342207", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1341342207" }, { "id": "rs1341342207", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1341342207" } ], "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": "5", "chr_pos": "55127266", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I327", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q86Y33-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q86Y33-1.314.314", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86Y33-1.408.408", "start_pos": 408, "end_pos": 408, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86Y33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs774926432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774926432", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774926432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774926432", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774926432", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774926432#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774926432", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774926432", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs774926432", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774926432", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ASAQGQPLKVITQSTAVKAM", "down_seq": "WCPWQSGVLAIGGGMKDGRL", "snv": [ { "evidence": [ { "id": "Q86Y33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33" }, { "id": "rs774926432", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774926432" }, { "id": "rs774926432", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774926432" }, { "id": "rs774926432", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774926432#frequency_tab" }, { "id": "rs774926432", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774926432" }, { "id": "rs774926432", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774926432" } ], "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 (DWC->NWC).", "chr_id": "5", "chr_pos": "55120544", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D408", "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": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "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": "Q86Y33-1.503.503", "start_pos": 503, "end_pos": 503, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86Y33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GGFFGHRGRVLHLSLSPDQT", "down_seq": "VFSAAADGTASVWNCY", "snv": [ { "evidence": [ { "id": "Q86Y33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86Y33" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "55114271", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R503", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q86Y33-1.519.519", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q86Y33-1.519.519", "start_pos": 519, "end_pos": 519, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs148916672", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148916672", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148916672", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs148916672", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs148916672", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148916672", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs148916672", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148916672#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs148916672", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148916672", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PDQTRVFSAAADGTASVWNC", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs148916672", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148916672" }, { "id": "rs148916672", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs148916672" }, { "id": "rs148916672", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148916672" }, { "id": "rs148916672", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148916672#frequency_tab" }, { "id": "rs148916672", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148916672" } ], "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 (NCY->NCC).", "chr_id": "5", "chr_pos": "55114222", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "Y519", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q86Y33-1.503.503", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86Y33-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748923654", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748923654", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748923654", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748923654", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748923654", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748923654", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "DFKSNFAKRLSAEVPVASSP", "down_seq": "TTRWQQSQTRALSSDSFGEE", "snv": [ { "evidence": [ { "id": "rs748923654", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748923654" }, { "id": "rs748923654", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748923654" }, { "id": "rs748923654", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748923654" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (ITT->NTT).", "chr_id": "5", "chr_pos": "55146765", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I73", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q86Y33-1.75.75", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q86Y33-1.80.80", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86Y33-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752729498", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752729498", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752729498", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752729498", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752729498", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752729498", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KRLSAEVPVASSPITTRWQQ", "down_seq": "QTRALSSDSFGEEQSTTYLP", "snv": [ { "evidence": [ { "id": "rs752729498", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752729498" }, { "id": "rs752729498", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752729498" }, { "id": "rs752729498", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752729498" } ], "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": "5", "chr_pos": "55146744", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S80", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q86Y33-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q86Y33-1.75.75", "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": "Q86Y33-1.364.364", "start_pos": 364, "end_pos": 364, "uniprot_canonical_ac": "Q86Y33-1", "length": 519, "uniprot_id": "CD20B_HUMAN", "protein_name": "Cell division cycle protein 20 homolog B", "refseq_ac": "NP_001139206", "refseq_name": "cell division cycle protein 20 homolog B isoform 2", "gene_name": "CDC20B", "gene_names_uniprotkb": "CDC20B; G6VTS76519", "gene_names_refseq": "CDC20B; G6VTS76519", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86Y33", "url": "https://www.uniprot.org/uniprotkb/Q86Y33" } ], "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": "Q86Y33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86Y33" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q86Y33", "url": "https://www.iedb.org/epitope/Q86Y33", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q86Y33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86Y33", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VAQHHVGTLRHKQAVCALKW", "down_seq": "PDGRLLSSGCSDGLLTIWPH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q86Y33", "url": "https://www.iedb.org/epitope/Q86Y33" }, { "database": "iPTMnet", "id": "Q86Y33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86Y33" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Ser364" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "364", "end_pos": "364" } ] } ], "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": "Q8IV32-1.268.268", "start_pos": 268, "end_pos": 268, "uniprot_canonical_ac": "Q8IV32-1", "length": 467, "uniprot_id": "CCD71_HUMAN", "protein_name": "Coiled-coil domain-containing protein 71", "refseq_ac": "NP_075054", "refseq_name": "coiled-coil domain-containing protein 71", "gene_name": "CCDC71", "gene_names_uniprotkb": "CCDC71", "gene_names_refseq": "CCDC71", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IV32", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV32", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PRRGSGHQSKTNRATGSPSV", "down_seq": "RMKGGSALGTKTAQAKVART", "snv": [ { "evidence": [ { "id": "Q8IV32", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV32" } ], "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": "49163407", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R268", "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": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "411", "end_pos": "411" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8IV32-1.269.269", "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": "Q8IV32-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "Q8IV32-1", "length": 467, "uniprot_id": "CCD71_HUMAN", "protein_name": "Coiled-coil domain-containing protein 71", "refseq_ac": "NP_075054", "refseq_name": "coiled-coil domain-containing protein 71", "gene_name": "CCDC71", "gene_names_uniprotkb": "CCDC71", "gene_names_refseq": "CCDC71", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IV32", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV32", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RRGSGHQSKTNRATGSPSVR", "down_seq": "MKGGSALGTKTAQAKVARTL", "snv": [ { "evidence": [ { "id": "Q8IV32", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV32" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "49163403", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R269", "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": "snv", "site_list": [ { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "411", "end_pos": "411" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8IV32-1.268.268", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IV32-1.317.317", "start_pos": 317, "end_pos": 317, "uniprot_canonical_ac": "Q8IV32-1", "length": 467, "uniprot_id": "CCD71_HUMAN", "protein_name": "Coiled-coil domain-containing protein 71", "refseq_ac": "NP_075054", "refseq_name": "coiled-coil domain-containing protein 71", "gene_name": "CCDC71", "gene_names_uniprotkb": "CCDC71", "gene_names_refseq": "CCDC71", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IV32", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV32", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "AKVARTQAKAAKARAKAKAA", "down_seq": "VKAKAKAKAAQVKAKAKVMA", "snv": [ { "evidence": [ { "id": "Q8IV32", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV32" } ], "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": "3", "chr_pos": "49163259", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q317", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "411", "end_pos": "411" } ] } ], "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": "Q8IV32-1.56.56", "start_pos": 56, "end_pos": 56, "uniprot_canonical_ac": "Q8IV32-1", "length": 467, "uniprot_id": "CCD71_HUMAN", "protein_name": "Coiled-coil domain-containing protein 71", "refseq_ac": "NP_075054", "refseq_name": "coiled-coil domain-containing protein 71", "gene_name": "CCDC71", "gene_names_uniprotkb": "CCDC71", "gene_names_refseq": "CCDC71", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IV32", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV32", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PMSQDLSATEAQLVAFLQGL", "down_seq": "DDGFQPTILRSGDVYGYSSC", "snv": [ { "evidence": [ { "id": "Q8IV32", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV32" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "49164042", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R56", "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" } ] }, { "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": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "411", "end_pos": "411" } ] } ], "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": "Q8IV32-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "Q8IV32-1", "length": 467, "uniprot_id": "CCD71_HUMAN", "protein_name": "Coiled-coil domain-containing protein 71", "refseq_ac": "NP_075054", "refseq_name": "coiled-coil domain-containing protein 71", "gene_name": "CCDC71", "gene_names_uniprotkb": "CCDC71", "gene_names_refseq": "CCDC71", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32" } ], "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": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32" }, { "database": "iPTMnet", "id": "Q8IV32", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV32" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IV32", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV32", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPAGRATLLPMPLSGRLAKA", "down_seq": "TPALAKHATTNLLLSSLKQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8IV32", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV32" } ], "site_lbl": "Ser129" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "411", "end_pos": "411" } ] } ], "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": "Q8IV32-1.411.411", "start_pos": 411, "end_pos": 411, "uniprot_canonical_ac": "Q8IV32-1", "length": 467, "uniprot_id": "CCD71_HUMAN", "protein_name": "Coiled-coil domain-containing protein 71", "refseq_ac": "NP_075054", "refseq_name": "coiled-coil domain-containing protein 71", "gene_name": "CCDC71", "gene_names_uniprotkb": "CCDC71", "gene_names_refseq": "CCDC71", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV32", "url": "https://www.uniprot.org/uniprotkb/Q8IV32" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class \u0399 Ligandome.", "journal": "Journal of proteome research", "date": "2019-04-05", "authors": "Demmers Laura C, Heck Albert J R, Wu Wei", "evidence": [ { "database": "iPTMnet", "id": "Q8IV32", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV32" } ], "reference": [ { "type": "PubMed", "id": "30784271", "url": "https://glygen.org/publication/PubMed/30784271" } ] } ], "crossref": [ { "id": "Q8IV32", "url": "https://www.iedb.org/epitope/Q8IV32", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q8IV32", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV32", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "30784271", "url": "https://glygen.org/publication/PubMed/30784271", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KRAEEAKDLPPKKRTRLGPR", "down_seq": "PKAWLGPGTAKLLKFRAIKV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q8IV32", "url": "https://www.iedb.org/epitope/Q8IV32" }, { "database": "iPTMnet", "id": "Q8IV32", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV32" }, { "database": "PubMed", "id": "30784271", "url": "https://glygen.org/publication/PubMed/30784271" } ], "site_lbl": "Ser411" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "411", "end_pos": "411" } ] } ], "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": "Q8IYL3-1.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "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": "1886", "url": "https://glyconnect.expasy.org/browser/proteins/1886" } ], "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": "1886", "url": "https://glyconnect.expasy.org/browser/proteins/1886", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "rs201090578", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201090578", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201090578", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201090578", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201090578", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201090578#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201090578", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201090578", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KTRDGLSVPKHSAGSGAEES", "down_seq": "SSSTVQKQNEPGLQTEDVQK", "glycosylation": [ { "glytoucan_ac": "G94854LT", "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": "Asn154", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1886", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1886" } ] } ], "snv": [ { "evidence": [ { "id": "rs201090578", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201090578" }, { "id": "rs201090578", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201090578" }, { "id": "rs201090578", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201090578#frequency_tab" }, { "id": "rs201090578", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201090578" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->DSS).", "chr_id": "1", "chr_pos": "3890727", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N154", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8IYL3-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IYL3-1.155.155", "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": "Q8IYL3-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "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": "Q8IYL3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q8IYL3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IYL3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IYL3", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "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": "Q8IYL3", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IYL3" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "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": "Q8IYL3-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IYL3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYL3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TRDGLSVPKHSAGSGAEESN", "down_seq": "SSTVQKQNEPGLQTEDVQKP", "snv": [ { "evidence": [ { "id": "Q8IYL3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYL3" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "1", "chr_pos": "3890723", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S155", "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": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8IYL3-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IYL3-1.154.154", "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": "Q8IYL3-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1638490373", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1638490373", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1638490373", "url": "https://www.ensembl.org/id/rs1638490373", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QKQNEPGLQTEDVQKPPLQM", "down_seq": "NSVFLDDDSNQPMPVSRFFG", "snv": [ { "evidence": [ { "id": "rs1638490373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1638490373" }, { "id": "rs1638490373", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1638490373" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DNS->NNS).", "chr_id": "1", "chr_pos": "3890649", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D180", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q8IYL3-1.189.189", "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": "Q8IYL3-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IYL3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYL3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AQEVAGSTSAKTACLTSSSH", "down_seq": "ATDTRTSKKFKCDKGHLVKS", "snv": [ { "evidence": [ { "id": "Q8IYL3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYL3" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "1", "chr_pos": "3891041", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K49", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "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": "Q8IYL3-1.96.96", "start_pos": 96, "end_pos": 96, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1638498452", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1638498452", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1638498452", "url": "https://www.ensembl.org/id/rs1638498452", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "PKNDSASLPKVTPETPCENE", "down_seq": "AEGSALLPGSEAGVSVQQGA", "snv": [ { "evidence": [ { "id": "rs1638498452", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1638498452" }, { "id": "rs1638498452", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1638498452" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEF->NES).", "chr_id": "1", "chr_pos": "3890900", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F96", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "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": "Q8IYL3-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" }, { "database": "iPTMnet", "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3", "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": "SDSRLAKTRDGLSVPKHSAG", "down_seq": "GAEESNSSSTVQKQNEPGLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser148" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8IYL3-1.154.154", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IYL3-1.155.155", "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": "Q8IYL3-1.189.189", "start_pos": 189, "end_pos": 189, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "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": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" }, { "database": "iPTMnet", "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" }, { "database": "iPTMnet", "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "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": "TEDVQKPPLQMDNSVFLDDD", "down_seq": "NQPMPVSRFFGNVELMQDLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser189" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IYL3-1.180.180", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IYL3-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "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": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] } ], "crossref": [ { "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSRKLTGAVRSSARLKARSC", "down_seq": "AARLASAQEVAGSTSAKTAC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ], "site_lbl": "Ser22" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8IYL3-1.28.28", "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": "Q8IYL3-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "Q8IYL3-1", "length": 243, "uniprot_id": "CA174_HUMAN", "protein_name": "UPF0688 protein C1orf174", "refseq_ac": "NP_997239", "refseq_name": "UPF0688 protein C1orf174", "gene_name": "C1orf174", "gene_names_uniprotkb": "C1orf174", "gene_names_refseq": "C1orf174", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYL3", "url": "https://www.uniprot.org/uniprotkb/Q8IYL3" } ], "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": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] } ], "crossref": [ { "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAVRSSARLKARSCSAARLA", "down_seq": "AQEVAGSTSAKTACLTSSSH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8IYL3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYL3" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ], "site_lbl": "Ser28" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "154", "end_pos": "154" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "28", "end_pos": "28" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8IYL3-1.22.22", "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": "Q8N6N3-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q8N6N3-1", "length": 182, "uniprot_id": "CA052_HUMAN", "protein_name": "UPF0690 protein C1orf52", "refseq_ac": "NP_932343", "refseq_name": "UPF0690 protein C1orf52", "gene_name": "C1orf52", "gene_names_uniprotkb": "C1orf52; BAG; GM117", "gene_names_refseq": "C1orf52; gm117", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" } ], "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": "Q8N6N3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8N6N3" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8N6N3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8N6N3", "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": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q8N6N3", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8N6N3" } ] } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "67", "end_pos": "67" } ] } ], "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": "Q8N6N3-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "Q8N6N3-1", "length": 182, "uniprot_id": "CA052_HUMAN", "protein_name": "UPF0690 protein C1orf52", "refseq_ac": "NP_932343", "refseq_name": "UPF0690 protein C1orf52", "gene_name": "C1orf52", "gene_names_uniprotkb": "C1orf52; BAG; GM117", "gene_names_refseq": "C1orf52; gm117", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" } ], "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": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "iPTMnet", "id": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455" } ] } ], "crossref": [ { "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TTEKKPPPPELDMAIKWSNI", "down_seq": "EDNGDDAPQNAKKARLLPEG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "PubMed", "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455" }, { "database": "iPTMnet", "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3" } ], "site_lbl": "Tyr132" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "67", "end_pos": "67" } ] } ], "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": "Q8N6N3-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "Q8N6N3-1", "length": 182, "uniprot_id": "CA052_HUMAN", "protein_name": "UPF0690 protein C1orf52", "refseq_ac": "NP_932343", "refseq_name": "UPF0690 protein C1orf52", "gene_name": "C1orf52", "gene_names_uniprotkb": "C1orf52; BAG; GM117", "gene_names_refseq": "C1orf52; gm117", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" } ], "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": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "iPTMnet", "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3" } ], "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": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "iPTMnet", "id": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "iPTMnet", "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "iPTMnet", "id": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "iPTMnet", "id": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.", "journal": "Journal of proteome research", "date": "2008", "authors": "Tsai CF, Wang YT, Chen YR, Lai CY, Lin PY, Pan KT, Chen JY, Khoo KH, Chen YJ", "evidence": [ { "database": "iPTMnet", "id": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "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": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "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": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3", "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DAPQNAKKARLLPEGEETLE", "down_seq": "DDEKDEHTSKKRKVEPGEPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser158" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "67", "end_pos": "67" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8N6N3-1.166.166", "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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8N6N3-1.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "Q8N6N3-1", "length": 182, "uniprot_id": "CA052_HUMAN", "protein_name": "UPF0690 protein C1orf52", "refseq_ac": "NP_932343", "refseq_name": "UPF0690 protein C1orf52", "gene_name": "C1orf52", "gene_names_uniprotkb": "C1orf52; BAG; GM117", "gene_names_refseq": "C1orf52; gm117", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" } ], "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": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "iPTMnet", "id": "Q8N6N3-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3", "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": "ARLLPEGEETLESDDEKDEH", "down_seq": "SKKRKVEPGEPAKKKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr166" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "67", "end_pos": "67" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8N6N3-1.158.158", "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": "Q8N6N3-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "Q8N6N3-1", "length": 182, "uniprot_id": "CA052_HUMAN", "protein_name": "UPF0690 protein C1orf52", "refseq_ac": "NP_932343", "refseq_name": "UPF0690 protein C1orf52", "gene_name": "C1orf52", "gene_names_uniprotkb": "C1orf52; BAG; GM117", "gene_names_refseq": "C1orf52; gm117", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" } ], "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": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "iPTMnet", "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GCRNKAEKRLPGPDELFRSV", "down_seq": "RPAFLYNPLNKQIDWERHVV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q8N6N3", "url": "https://www.uniprot.org/uniprotkb/Q8N6N3" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8N6N3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8N6N3" } ], "site_lbl": "Thr67" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "67", "end_pos": "67" } ] } ], "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": "Q8WWL7-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "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": "Q8WWL7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WWL7" } ], "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": "Q8WWL7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WWL7", "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": "Q8WWL7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WWL7" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "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": "Q8WWL7-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KISPSSLQESPSSLQGALKK", "down_seq": "SAFEDLTNASQCQPVQPKKE", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "In cycB3XA; prevents its destruction after completion of anaphase; when associated with A-63 and A-68.", "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8WWL7-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WWL7-1.68.68", "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": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WWL7-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "PSSLQESPSSLQGALKKRSA", "down_seq": "EDLTNASQCQPVQPKKEANK", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "In cycB3XA; prevents its destruction after completion of anaphase; when associated with A-60 and A-68.", "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8WWL7-1.60.60", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WWL7-1.68.68", "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": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WWL7-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ESPSSLQGALKKRSAFEDLT", "down_seq": "ASQCQPVQPKKEANKEFVKV", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "In cycB3XA; prevents its destruction after completion of anaphase; when associated with A-60 and A-63.", "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8WWL7-1.60.60", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WWL7-1.63.63", "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": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WWL7-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WWL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WWL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EEVSLLEKLQPLQEESDSDD", "down_seq": "FVIEPMTFKKTHKTEEAAIT", "snv": [ { "evidence": [ { "id": "Q8WWL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WWL7" } ], "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": "23", "chr_pos": "50308783", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A205", "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": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "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": "Q8WWL7-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WWL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WWL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HKLSSLKKKCTIYGKICHFR", "down_seq": "PPVLQTTICGAMSSIKKPTT", "snv": [ { "evidence": [ { "id": "Q8WWL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WWL7" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "23", "chr_pos": "50309072", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K301", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "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": "Q8WWL7-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WWL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WWL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VPKKSQSSKIVPSHHDPSEK", "down_seq": "GENCQTKISPSSLQESPSSL", "snv": [ { "evidence": [ { "id": "Q8WWL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WWL7" } ], "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": "23", "chr_pos": "50288781", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T33", "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: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": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "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": "Q8WWL7-1.626.626", "start_pos": 626, "end_pos": 626, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WWL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WWL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "VLQKITSEEESFYKKLLPFK", "down_seq": "KSTTEEKFLSQEPSALKEKH", "snv": [ { "evidence": [ { "id": "Q8WWL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WWL7" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "50310047", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "M626", "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": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "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": "Q8WWL7-1.1038.1038", "start_pos": 1038, "end_pos": 1038, "uniprot_canonical_ac": "Q8WWL7-1", "length": 1395, "uniprot_id": "CCNB3_HUMAN", "protein_name": "G2/mitotic-specific cyclin-B3", "refseq_ac": "NP_149020", "refseq_name": "G2/mitotic-specific cyclin-B3 isoform 3", "gene_name": "CCNB3", "gene_names_uniprotkb": "CCNB3; CYCB3", "gene_names_refseq": "CCNB3; CYCB3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WWL7", "url": "https://www.uniprot.org/uniprotkb/Q8WWL7" } ], "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": "Q8WWL7-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WWL7-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q8WWL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WWL7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KPTTGKELSFKEPLALQESP", "down_seq": "CKEDTFLETFLIPQIGTSPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WWL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WWL7" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Thr1038" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "60", "end_pos": "60" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] }, { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "626", "end_pos": "626" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1038", "end_pos": "1038" } ] } ], "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": "Q96HJ3-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q96HJ3-1", "length": 373, "uniprot_id": "CCD34_HUMAN", "protein_name": "Coiled-coil domain-containing protein 34", "refseq_ac": "NP_110398", "refseq_name": "coiled-coil domain-containing protein 34 isoform 1", "gene_name": "CCDC34", "gene_names_uniprotkb": "CCDC34; L15; RAMA3", "gene_names_refseq": "CCDC34; L15; NY-REN-41; RAMA3; SPGF76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96HJ3", "url": "https://www.uniprot.org/uniprotkb/Q96HJ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q96HJ3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96HJ3" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96HJ3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96HJ3", "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": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "Q96HJ3", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96HJ3" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "343", "end_pos": "343" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "52", "end_pos": "52" } ] } ], "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": "Q96HJ3-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q96HJ3-1", "length": 373, "uniprot_id": "CCD34_HUMAN", "protein_name": "Coiled-coil domain-containing protein 34", "refseq_ac": "NP_110398", "refseq_name": "coiled-coil domain-containing protein 34 isoform 1", "gene_name": "CCDC34", "gene_names_uniprotkb": "CCDC34; L15; RAMA3", "gene_names_refseq": "CCDC34; L15; NY-REN-41; RAMA3; SPGF76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96HJ3", "url": "https://www.uniprot.org/uniprotkb/Q96HJ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96HJ3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96HJ3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "NAEECERKKKEKEKEKQQQA", "down_seq": "IQEKKEIAEKKFQEWLENAK", "snv": [ { "evidence": [ { "id": "Q96HJ3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96HJ3" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "27340812", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "E264", "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: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": "264", "end_pos": "264" }, { "start_pos": "343", "end_pos": "343" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "52", "end_pos": "52" } ] } ], "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": "Q96HJ3-1.343.343", "start_pos": 343, "end_pos": 343, "uniprot_canonical_ac": "Q96HJ3-1", "length": 373, "uniprot_id": "CCD34_HUMAN", "protein_name": "Coiled-coil domain-containing protein 34", "refseq_ac": "NP_110398", "refseq_name": "coiled-coil domain-containing protein 34 isoform 1", "gene_name": "CCDC34", "gene_names_uniprotkb": "CCDC34; L15; RAMA3", "gene_names_refseq": "CCDC34; L15; NY-REN-41; RAMA3; SPGF76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96HJ3", "url": "https://www.uniprot.org/uniprotkb/Q96HJ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96HJ3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96HJ3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PIHMPPPKEAKDLSGRKSKR", "down_seq": "VISQPHKSSSLVIHKARSNL", "snv": [ { "evidence": [ { "id": "Q96HJ3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96HJ3" } ], "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": "11", "chr_pos": "27338915", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P343", "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": "264", "end_pos": "264" }, { "start_pos": "343", "end_pos": "343" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "52", "end_pos": "52" } ] } ], "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": "Q96HJ3-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "Q96HJ3-1", "length": 373, "uniprot_id": "CCD34_HUMAN", "protein_name": "Coiled-coil domain-containing protein 34", "refseq_ac": "NP_110398", "refseq_name": "coiled-coil domain-containing protein 34 isoform 1", "gene_name": "CCDC34", "gene_names_uniprotkb": "CCDC34; L15; RAMA3", "gene_names_refseq": "CCDC34; L15; NY-REN-41; RAMA3; SPGF76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96HJ3", "url": "https://www.uniprot.org/uniprotkb/Q96HJ3" } ], "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": "Q96HJ3", "url": "https://www.uniprot.org/uniprotkb/Q96HJ3" }, { "database": "iPTMnet", "id": "Q96HJ3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96HJ3" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q96HJ3", "url": "https://www.uniprot.org/uniprotkb/Q96HJ3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96HJ3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96HJ3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SCSVPMTGARGQGLEVVRSP", "down_seq": "PPLPLSCSNSTRSLLSPLGH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96HJ3", "url": "https://www.uniprot.org/uniprotkb/Q96HJ3" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q96HJ3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96HJ3" } ], "site_lbl": "Ser52" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "343", "end_pos": "343" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "52", "end_pos": "52" } ] } ], "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": "Q96KC9-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "ADMSNYNSSIKSNVPADEAV", "down_seq": "VTDSTIPEAEIPPAPEESFT", "snv": [ { "evidence": [ { "id": "Q96KC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "70335657", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q206", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "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": "Q96KC9-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PEESFTTIPDITALEEEKIT", "down_seq": "IDLSVLEDDTSAVATLTDSD", "snv": [ { "evidence": [ { "id": "Q96KC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9" } ], "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": "4", "chr_pos": "70335760", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E241", "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: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: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": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "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": "Q96KC9-1.324.324", "start_pos": 324, "end_pos": 324, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ANEAETHSVLLTAVESRYDF", "down_seq": "VPASIATNLVEESSTEEDLS", "snv": [ { "evidence": [ { "id": "Q96KC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "3", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "70336009", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V324", "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: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": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q96KC9-1.319.319", "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": "Q96KC9-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "YMLESDFSTTTDNKLTAKKE", "down_seq": "LKSEDDMGTDFIKSTTHLQK", "snv": [ { "evidence": [ { "id": "Q96KC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "70335261", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K74", "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": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q96KC9-1.84.84", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96KC9-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TDNKLTAKKEKLKSEDDMGT", "down_seq": "FIKSTTHLQKEITSLTGTTN", "snv": [ { "evidence": [ { "id": "Q96KC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96KC9" } ], "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 (3).", "chr_id": "4", "chr_pos": "70335289", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D84", "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" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q96KC9-1.74.74", "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": "Q96KC9-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AVATLTDSDEKFITVFELTT", "down_seq": "AEKDKDKREDTLLTDEETTE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "site_lbl": "Ser273" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q96KC9-1.287.287", "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": "Q96KC9-1.287.287", "start_pos": 287, "end_pos": 287, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VFELTTSAEKDKDKREDTLL", "down_seq": "DEETTEGASIWMERDTANEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by CK2", "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "site_lbl": "Thr287" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q96KC9-1.273.273", "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": "Q96KC9-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MERDTANEAETHSVLLTAVE", "down_seq": "RYDFVVPASIATNLVEESST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "site_lbl": "Ser319" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q96KC9-1.324.324", "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": "Q96KC9-1.376.376", "start_pos": 376, "end_pos": 376, "uniprot_canonical_ac": "Q96KC9-1", "length": 395, "uniprot_id": "CABS1_HUMAN", "protein_name": "Calcium-binding and spermatid-specific protein 1", "refseq_ac": "NP_149113", "refseq_name": "calcium-binding and spermatid-specific protein 1", "gene_name": "CABS1", "gene_names_uniprotkb": "CABS1; C4orf35", "gene_names_refseq": "C4orf35; CABS1; CLPH; NYD-SP26", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TEPFSGTTSVLDTPDYKEDT", "down_seq": "TTETDIFELLKEEPDEFMI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96KC9", "url": "https://www.uniprot.org/uniprotkb/Q96KC9" } ], "site_lbl": "Ser376" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "376", "end_pos": "376" } ] } ], "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": "Q96LT6-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "Q96LT6-1", "length": 269, "uniprot_id": "CA074_HUMAN", "protein_name": "UPF0739 protein C1orf74", "refseq_ac": "NP_689698", "refseq_name": "UPF0739 protein C1orf74", "gene_name": "C1orf74", "gene_names_uniprotkb": "C1orf74", "gene_names_refseq": "C1orf74; URLC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LT6", "url": "https://www.uniprot.org/uniprotkb/Q96LT6" } ], "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": "Q96LT6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96LT6" }, { "database": "O-GlcNAc Atlas", "id": "Q96LT6", "url": "https://oglcnac.org/atlas/detail/Q96LT6" } ], "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": "Q96LT6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96LT6", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "Q96LT6", "url": "https://oglcnac.org/atlas/detail/Q96LT6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1383551921", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1383551921", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1383551921", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1383551921", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q96LT6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LT6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LRVFTARISWLLGQPPILLY", "down_seq": "FSVPESLFPGLRDILNTWEK", "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": "Ser220", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "Q96LT6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96LT6" }, { "id": "Q96LT6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q96LT6" } ] } ], "snv": [ { "evidence": [ { "id": "rs1383551921", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1383551921" }, { "id": "rs1383551921", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1383551921" } ], "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": "209782976", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S220", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q96LT6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LT6" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->Y).", "chr_id": "1", "chr_pos": "209782976", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S220", "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": "220", "end_pos": "220" } ] }, { "type": "snv", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q96LT6-1.238.238", "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", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LT6-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "Q96LT6-1", "length": 269, "uniprot_id": "CA074_HUMAN", "protein_name": "UPF0739 protein C1orf74", "refseq_ac": "NP_689698", "refseq_name": "UPF0739 protein C1orf74", "gene_name": "C1orf74", "gene_names_uniprotkb": "C1orf74", "gene_names_refseq": "C1orf74; URLC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LT6", "url": "https://www.uniprot.org/uniprotkb/Q96LT6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LT6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LT6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AEIITHLQGLQRDLSLAVSY", "down_seq": "RLHSSDWNLCTVFGILLGYP", "snv": [ { "evidence": [ { "id": "Q96LT6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LT6" } ], "glycoeffect": [ "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: num. of cancers (3).", "chr_id": "1", "chr_pos": "209783156", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S160", "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": "220", "end_pos": "220" } ] }, { "type": "snv", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "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": "Q96LT6-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "Q96LT6-1", "length": 269, "uniprot_id": "CA074_HUMAN", "protein_name": "UPF0739 protein C1orf74", "refseq_ac": "NP_689698", "refseq_name": "UPF0739 protein C1orf74", "gene_name": "C1orf74", "gene_names_uniprotkb": "C1orf74", "gene_names_refseq": "C1orf74; URLC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LT6", "url": "https://www.uniprot.org/uniprotkb/Q96LT6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LT6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LT6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "LYSFSVPESLFPGLRDILNT", "down_seq": "EKDLRTRFRTQNDFADLSIS", "snv": [ { "evidence": [ { "id": "Q96LT6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LT6" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTW->NTC).", "chr_id": "1", "chr_pos": "209782921", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "W238", "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": "220", "end_pos": "220" } ] }, { "type": "snv", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q96LT6-1.220.220", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q96LT6-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q96LT6-1.254.254", "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": "Q96LT6-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "Q96LT6-1", "length": 269, "uniprot_id": "CA074_HUMAN", "protein_name": "UPF0739 protein C1orf74", "refseq_ac": "NP_689698", "refseq_name": "UPF0739 protein C1orf74", "gene_name": "C1orf74", "gene_names_uniprotkb": "C1orf74", "gene_names_refseq": "C1orf74; URLC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LT6", "url": "https://www.uniprot.org/uniprotkb/Q96LT6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777893458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777893458", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777893458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777893458", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777893458", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777893458#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777893458", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777893458", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "RDILNTWEKDLRTRFRTQND", "down_seq": "ADLSISSEIVTLPAVAL", "snv": [ { "evidence": [ { "id": "rs777893458", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777893458" }, { "id": "rs777893458", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777893458" }, { "id": "rs777893458", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777893458#frequency_tab" }, { "id": "rs777893458", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777893458" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDF->NDC).", "chr_id": "1", "chr_pos": "209782880", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F252", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] }, { "type": "snv", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q96LT6-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96LT6-1.254.254", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LT6-1.254.254", "start_pos": 254, "end_pos": 254, "uniprot_canonical_ac": "Q96LT6-1", "length": 269, "uniprot_id": "CA074_HUMAN", "protein_name": "UPF0739 protein C1orf74", "refseq_ac": "NP_689698", "refseq_name": "UPF0739 protein C1orf74", "gene_name": "C1orf74", "gene_names_uniprotkb": "C1orf74", "gene_names_refseq": "C1orf74; URLC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LT6", "url": "https://www.uniprot.org/uniprotkb/Q96LT6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LT6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LT6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ILNTWEKDLRTRFRTQNDFA", "down_seq": "LSISSEIVTLPAVAL", "snv": [ { "evidence": [ { "id": "Q96LT6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LT6" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "1", "chr_pos": "209782875", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D254", "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": "220", "end_pos": "220" } ] }, { "type": "snv", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q96LT6-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96LT6-1.252.252", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LT6-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "Q96LT6-1", "length": 269, "uniprot_id": "CA074_HUMAN", "protein_name": "UPF0739 protein C1orf74", "refseq_ac": "NP_689698", "refseq_name": "UPF0739 protein C1orf74", "gene_name": "C1orf74", "gene_names_uniprotkb": "C1orf74", "gene_names_refseq": "C1orf74; URLC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LT6", "url": "https://www.uniprot.org/uniprotkb/Q96LT6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1427910296", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427910296", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1427910296", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1427910296#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1427910296", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427910296", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GEVLAVARGLKPAVLYDCNC", "down_seq": "GASELQSYLEELKGLGFLTF", "snv": [ { "evidence": [ { "id": "rs1427910296", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427910296" }, { "id": "rs1427910296", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1427910296#frequency_tab" }, { "id": "rs1427910296", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427910296" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCA->NCS).", "chr_id": "1", "chr_pos": "209783454", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A61", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1427910296", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427910296" }, { "id": "rs1427910296", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1427910296#frequency_tab" }, { "id": "rs1427910296", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427910296" } ], "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": "1", "chr_pos": "209783454", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A61", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] }, { "type": "snv", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "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": 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": "Q96P09-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "Q96P09-1", "length": 236, "uniprot_id": "BIRC8_HUMAN", "protein_name": "Baculoviral IAP repeat-containing protein 8", "refseq_ac": "", "refseq_name": "", "gene_name": "BIRC8", "gene_names_uniprotkb": "BIRC8; ILP2", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96P09", "url": "https://www.uniprot.org/uniprotkb/Q96P09" } ], "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": "Q96P09", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96P09" }, { "database": "O-GlcNAc Atlas", "id": "Q96P09", "url": "https://oglcnac.org/atlas/detail/Q96P09" } ], "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": "Q96P09", "url": "https://oglcnac.org/atlas/detail/Q96P09", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GHEYINNIHLTRSLEGALVQ", "down_seq": "TKKTPSLTKRISDTIFPNPM", "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": "Thr94", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q96P09", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q96P09" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q96P09-1.95.95", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96P09-1.95.95", "start_pos": 95, "end_pos": 95, "uniprot_canonical_ac": "Q96P09-1", "length": 236, "uniprot_id": "BIRC8_HUMAN", "protein_name": "Baculoviral IAP repeat-containing protein 8", "refseq_ac": "", "refseq_name": "", "gene_name": "BIRC8", "gene_names_uniprotkb": "BIRC8; ILP2", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96P09", "url": "https://www.uniprot.org/uniprotkb/Q96P09" } ], "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": "Q96P09", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96P09" }, { "database": "O-GlcNAc Atlas", "id": "Q96P09", "url": "https://oglcnac.org/atlas/detail/Q96P09" } ], "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": "Q96P09", "url": "https://oglcnac.org/atlas/detail/Q96P09", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HEYINNIHLTRSLEGALVQT", "down_seq": "KKTPSLTKRISDTIFPNPML", "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": "Thr95", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q96P09", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q96P09" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q96P09-1.94.94", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96P09-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q96P09-1", "length": 236, "uniprot_id": "BIRC8_HUMAN", "protein_name": "Baculoviral IAP repeat-containing protein 8", "refseq_ac": "", "refseq_name": "", "gene_name": "BIRC8", "gene_names_uniprotkb": "BIRC8; ILP2", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96P09", "url": "https://www.uniprot.org/uniprotkb/Q96P09" } ], "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": "Q96P09", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96P09" }, { "database": "O-GlcNAc Atlas", "id": "Q96P09", "url": "https://oglcnac.org/atlas/detail/Q96P09" } ], "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": "Q96P09", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96P09", "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": "Q96P09", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96P09" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "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": "Q9BXU9-2.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "Q9BXU9-2", "length": 261, "uniprot_id": "CABP8_HUMAN", "protein_name": "Calcium-binding protein 8", "refseq_ac": "NP_001017440", "refseq_name": "calcium-binding protein 8 isoform 2", "gene_name": "CALN1", "gene_names_uniprotkb": "CALN1; CABP8", "gene_names_refseq": "CABP8; CALN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXU9", "url": "https://www.uniprot.org/uniprotkb/Q9BXU9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXU9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MRLPEQPGEGKP", "down_seq": "NEKKGDGGALGGGEEPPRSQ", "snv": [ { "evidence": [ { "id": "Q9BXU9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9" } ], "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 (3).", "chr_id": "7", "chr_pos": "72403333", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E13", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "13", "end_pos": "13" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "88", "end_pos": "88" }, { "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": "Q9BXU9-2.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "Q9BXU9-2", "length": 261, "uniprot_id": "CABP8_HUMAN", "protein_name": "Calcium-binding protein 8", "refseq_ac": "NP_001017440", "refseq_name": "calcium-binding protein 8 isoform 2", "gene_name": "CALN1", "gene_names_uniprotkb": "CALN1; CABP8", "gene_names_refseq": "CABP8; CALN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXU9", "url": "https://www.uniprot.org/uniprotkb/Q9BXU9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXU9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VDFDEFMTILGPKLVSSEGR", "down_seq": "GFLGNTIDSIFWQFDMQRIT", "snv": [ { "evidence": [ { "id": "Q9BXU9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "72023698", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D154", "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": "13", "end_pos": "13" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "88", "end_pos": "88" }, { "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": "Q9BXU9-2.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "Q9BXU9-2", "length": 261, "uniprot_id": "CABP8_HUMAN", "protein_name": "Calcium-binding protein 8", "refseq_ac": "NP_001017440", "refseq_name": "calcium-binding protein 8 isoform 2", "gene_name": "CALN1", "gene_names_uniprotkb": "CALN1; CABP8", "gene_names_refseq": "CABP8; CALN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXU9", "url": "https://www.uniprot.org/uniprotkb/Q9BXU9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXU9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NCQTEFEGVHSQKQNRQTCV", "down_seq": "KSLICAFAMAFIISVMLIAA", "snv": [ { "evidence": [ { "id": "Q9BXU9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9" } ], "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 (3).", "chr_id": "7", "chr_pos": "71787866", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R232", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "13", "end_pos": "13" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9BXU9-2.238.238", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXU9-2.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "Q9BXU9-2", "length": 261, "uniprot_id": "CABP8_HUMAN", "protein_name": "Calcium-binding protein 8", "refseq_ac": "NP_001017440", "refseq_name": "calcium-binding protein 8 isoform 2", "gene_name": "CALN1", "gene_names_uniprotkb": "CALN1; CABP8", "gene_names_refseq": "CABP8; CALN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXU9", "url": "https://www.uniprot.org/uniprotkb/Q9BXU9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXU9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EGVHSQKQNRQTCVRKSLIC", "down_seq": "FAMAFIISVMLIAANQILRS", "snv": [ { "evidence": [ { "id": "Q9BXU9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "71787849", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A238", "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: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": "snv", "site_list": [ { "start_pos": "13", "end_pos": "13" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9BXU9-2.232.232", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9BXU9-2.257.257", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXU9-2.257.257", "start_pos": 257, "end_pos": 257, "uniprot_canonical_ac": "Q9BXU9-2", "length": 261, "uniprot_id": "CABP8_HUMAN", "protein_name": "Calcium-binding protein 8", "refseq_ac": "NP_001017440", "refseq_name": "calcium-binding protein 8 isoform 2", "gene_name": "CALN1", "gene_names_uniprotkb": "CALN1; CABP8", "gene_names_refseq": "CABP8; CALN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXU9", "url": "https://www.uniprot.org/uniprotkb/Q9BXU9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXU9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CAFAMAFIISVMLIAANQIL", "down_seq": "SGME", "snv": [ { "evidence": [ { "id": "Q9BXU9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "71787791", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R257", "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: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": "13", "end_pos": "13" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9BXU9-2.238.238", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXU9-2.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "Q9BXU9-2", "length": 261, "uniprot_id": "CABP8_HUMAN", "protein_name": "Calcium-binding protein 8", "refseq_ac": "NP_001017440", "refseq_name": "calcium-binding protein 8 isoform 2", "gene_name": "CALN1", "gene_names_uniprotkb": "CALN1; CABP8", "gene_names_refseq": "CABP8; CALN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXU9", "url": "https://www.uniprot.org/uniprotkb/Q9BXU9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXU9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SAGSDSEQLANISVEELDEI", "down_seq": "EAFRVLDRDGNGFISKQELG", "snv": [ { "evidence": [ { "id": "Q9BXU9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "72106288", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R84", "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: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": "13", "end_pos": "13" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q9BXU9-2.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BXU9-2.92.92", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXU9-2.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "Q9BXU9-2", "length": 261, "uniprot_id": "CABP8_HUMAN", "protein_name": "Calcium-binding protein 8", "refseq_ac": "NP_001017440", "refseq_name": "calcium-binding protein 8 isoform 2", "gene_name": "CALN1", "gene_names_uniprotkb": "CALN1; CABP8", "gene_names_refseq": "CABP8; CALN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXU9", "url": "https://www.uniprot.org/uniprotkb/Q9BXU9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXU9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DSEQLANISVEELDEIREAF", "down_seq": "VLDRDGNGFISKQELGMAMR", "snv": [ { "evidence": [ { "id": "Q9BXU9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "7", "chr_pos": "72106276", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R88", "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: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": "13", "end_pos": "13" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q9BXU9-2.84.84", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BXU9-2.92.92", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXU9-2.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "Q9BXU9-2", "length": 261, "uniprot_id": "CABP8_HUMAN", "protein_name": "Calcium-binding protein 8", "refseq_ac": "NP_001017440", "refseq_name": "calcium-binding protein 8 isoform 2", "gene_name": "CALN1", "gene_names_uniprotkb": "CALN1; CABP8", "gene_names_refseq": "CABP8; CALN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXU9", "url": "https://www.uniprot.org/uniprotkb/Q9BXU9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXU9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LANISVEELDEIREAFRVLD", "down_seq": "DGNGFISKQELGMAMRSLGY", "snv": [ { "evidence": [ { "id": "Q9BXU9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXU9" } ], "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 (4).", "chr_id": "7", "chr_pos": "72106264", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R92", "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" } ] }, { "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": "13", "end_pos": "13" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BXU9-2.84.84", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BXU9-2.88.88", "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": "Q9H5V8-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] } ], "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": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GPCPFGEVQLQPSTSLLPTL", "down_seq": "RTFIWDVKAHKSIGLELQFS", "glycosylation": [ { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NIDCMSGPCPFGEVQLQPSTSLLPTLnR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn122", "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": "NIDCMSGPCPFGEVQLQPSTSLLPTLnR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn122", "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": "NIDCMSGPCPFGEVQLQPSTSLLPTLnR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn122", "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": "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": "Asn122", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "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": "Asn122", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "Q9H5V8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "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": 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" ] }, { "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": 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": 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": "Q9H5V8-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "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": "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": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "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": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "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" ] }, { "id": "rs754300803", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754300803", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754300803", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754300803", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754300803", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754300803", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs754300803", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754300803", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1698706368", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1698706368", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1698706368", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1698706368#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "THSISGRIDATVVRIGTFCS", "down_seq": "GTVSRIKMQEGVKMALHLPW", "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": "Asn180", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IGTFCSnGTVSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn180", "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": "IGTFCSnGTVSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn180", "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": "Asn180", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "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": "Asn180", "evidence": [ { "id": "Q9H5V8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8#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" } ] } ], "snv": [ { "evidence": [ { "id": "rs754300803", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754300803" }, { "id": "rs754300803", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754300803" }, { "id": "rs754300803", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754300803" }, { "id": "rs754300803", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754300803" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NGT->SGT).", "chr_id": "3", "chr_pos": "45112199", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N180", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1698706368", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1698706368" }, { "id": "rs1698706368", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1698706368#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGT->YGT).", "chr_id": "3", "chr_pos": "45112200", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N180", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9H5V8-1.168.168", "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" ] }, { "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": 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": 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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H5V8-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ], "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": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RIKMQEGVKMALHLPWFHPR", "down_seq": "VSGFSIANRSSIKRLCIIES", "glycosylation": [ { "glytoucan_ac": "G70101JE", "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": "Asn205", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "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": "Asn205", "evidence": [ { "id": "Q9H5V8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H5V8-1.207.207", "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" ] }, { "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": "Q9H5V8-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ], "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": "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": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160", "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": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "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": "rs553974292", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553974292", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs553974292", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs553974292", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs553974292", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553974292", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs553974292", "url": "https://www.ncbi.nlm.nih.gov/snp/rs553974292#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs553974292", "url": "http://gnomad.broadinstitute.org/awesome?query=rs553974292", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MTWQFVVPAHLRASVSFLNF", "down_seq": "LSNCERKEERVEYYIPGSTT", "glycosylation": [ { "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": "Asn270", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G39446WN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "ASVSFLNFNLSNCER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn270", "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": "Asn270", "evidence": [ { "id": "Q9H5V8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8#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" } ] } ], "snv": [ { "evidence": [ { "id": "rs553974292", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553974292" }, { "id": "rs553974292", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs553974292" }, { "id": "rs553974292", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553974292" }, { "id": "rs553974292", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs553974292#frequency_tab" }, { "id": "rs553974292", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs553974292" } ], "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 (NLS->SLS); n-glyco-sequon-gain (NFN->NFS).", "chr_id": "3", "chr_pos": "45110688", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N270", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs553974292", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553974292" }, { "id": "rs553974292", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs553974292" }, { "id": "rs553974292", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553974292" }, { "id": "rs553974292", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs553974292#frequency_tab" }, { "id": "rs553974292", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs553974292" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NLS->TLS); n-glyco-sequon-gain (NFN->NFT).", "chr_id": "3", "chr_pos": "45110688", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N270", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H5V8-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9H5V8-1.281.296", "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": 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", "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": 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", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H5V8-1.281.296", "start_pos": 281, "end_pos": 296, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "VEYYIPGSTTNPEVFK", "start_aa": "V", "up_seq": "RASVSFLNFNLSNCERKEER", "down_seq": "LEDKQPGNMAGNFNLSLQGC", "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": "VEYYIPGSTTNPEVFK", "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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9H5V8-1.270.270", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9H5V8-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9H5V8-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9H5V8-1.310.310", "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": 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": "Q9H5V8-1.310.310", "start_pos": 310, "end_pos": 310, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] } ], "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": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TNPEVFKLEDKQPGNMAGNF", "down_seq": "LSLQGCDQDAQSPGILRLQF", "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": "QPGNMAGNFnLSLQGCDQDAQSPGILR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn310", "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": "G05724UK", "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": "Asn310", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G06110VR", "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": "Asn310", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QPGNMAGNFnLSLQGCDQDAQSPGILR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn310", "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": "QPGNMAGNFnLSLQGCDQDAQSPGILR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn310", "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": "QPGNMAGNFnLSLQGCDQDAQSPGILR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn310", "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": "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": "Asn310", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G70101JE", "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": "Asn310", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "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": "Asn310", "evidence": [ { "id": "Q9H5V8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9H5V8-1.281.296", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9H5V8-1.306.306", "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": 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": 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": "Q9H5V8-1.339.339", "start_pos": 339, "end_pos": 339, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DAQSPGILRLQFQVLVQHPQ", "down_seq": "ESNKIYVVDLSNERAMSLTI", "glycosylation": [ { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LQFQVLVQHPQnESNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn339", "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": "LQFQVLVQHPQnESNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn339", "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": "Asn339", "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H5V8-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9H5V8-1.344.344", "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": 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", "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": 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", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H5V8-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "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": "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": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "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" ] }, { "id": "rs1272493694", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272493694", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1272493694", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1272493694#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1272493694", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272493694", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QSRKFVPGCFVCLESRTCSS", "down_seq": "LTLTSGSKHKISFLCDDLTR", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "TCSSnLTLTSGSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn386", "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": "Asn386", "evidence": [ { "id": "Q9H5V8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8#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" } ] } ], "snv": [ { "evidence": [ { "id": "rs1272493694", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272493694" }, { "id": "rs1272493694", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1272493694#frequency_tab" }, { "id": "rs1272493694", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272493694" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->TLT).", "chr_id": "3", "chr_pos": "45095436", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N386", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H5V8-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9H5V8-1.396.396", "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": 13 }, { "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": 13 } ], "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": 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": 13 }, { "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": 13 } ], "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": "Q9H5V8-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ], "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": "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": "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": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160", "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": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "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": "GAARLPRGAEAFEIALPRES", "down_seq": "ITVLIKLGTPTLLAKPCYIV", "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": "ESnITVLIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn39", "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": "ESnITVLIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn39", "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": "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": "Asn39", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "ESnITVLIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn39", "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": "ESnITVLIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn39", "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": "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": "Asn39", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "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": "Asn39", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "ESnITVLIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn39", "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": "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": "Asn39", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "ESnITVLIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn39", "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": "ESNITVLIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn39", "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": "G82463GQ", "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": "Asn39", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "ESnITVLIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn39", "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": "Asn39", "evidence": [ { "id": "Q9H5V8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8#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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H5V8-1.41.41", "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": 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": 13 }, { "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": 13 } ], "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": 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": 13 }, { "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": 13 } ], "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": "Q9H5V8-1.512.512", "start_pos": 512, "end_pos": 512, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ], "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": "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": "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": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160", "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": "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": "DLYFGSFCPGGSIKQIQVKQ", "down_seq": "ISVTLRTFAPSFQQEASRQG", "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": "QnISVTLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn512", "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": "G05724UK", "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": "Asn512", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QnISVTLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn512", "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": "QNISVTLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn512", "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": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QnISVTLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn512", "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": "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": "Asn512", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G92050GC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QnISVTLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn512", "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": "Asn512", "evidence": [ { "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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H5V8-1.514.514", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9H5V8-1.518.518", "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": 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": 7 }, { "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": 7 } ], "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": 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": 7 }, { "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": 7 } ], "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": "Q9H5V8-1.577.577", "start_pos": 577, "end_pos": 577, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] } ], "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": "1160", "url": "https://glyconnect.expasy.org/browser/proteins/1160", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VYLRTPNWDRGLPSLTSVSW", "down_seq": "ISVPRDQVACLTFFKERSGV", "glycosylation": [ { "glytoucan_ac": "G25079LO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GLPSLTSVSWnISVPR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn577", "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": "G46503DX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TPNWDRGLPSLTSVSWnISVPR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn577", "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": "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": "Asn577", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GLPSLTSVSWnISVPR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn577", "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": "G70101JE", "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": "Asn577", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1160", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1160" } ] }, { "glytoucan_ac": "G72747WU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TPNWDRGLPSLTSVSWnISVPR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn577", "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": "GLPSLTSVSWnISVPR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn577", "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": "TPNWDRGLPSLTSVSWnISVPR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn577", "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": "Asn577", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H5V8-1.579.579", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9H5V8-1.589.589", "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": 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": 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": "Q9H5V8-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q9H5V8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] } ], "crossref": [ { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H5V8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H5V8", "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": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "Q9H5V8", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H5V8" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "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": "Q9H5V8-1.734.734", "start_pos": 734, "end_pos": 734, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The C2 domain of PKCdelta is a phosphotyrosine binding domain.", "journal": "Cell", "date": "2005", "authors": "Benes CH, Wu N, Elia AE, Dharia T, Cantley LC, Soltoff SP", "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "15851033", "url": "https://glygen.org/publication/PubMed/15851033" } ] }, { "title": "Adhesion or plasmin regulates tyrosine phosphorylation of a novel membrane glycoprotein p80/gp140/CUB domain-containing protein 1 in epithelia.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Brown TA, Yang TM, Zaitsevskaia T, Xia Y, Dunn CA, Sigle RO, Knudsen B, Carter WG", "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" }, { "database": "iPTMnet", "id": "Q9H5V8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8-1" } ], "reference": [ { "type": "PubMed", "id": "14739293", "url": "https://glygen.org/publication/PubMed/14739293" } ] }, { "title": "Cellular settings mediating Src Substrate switching between focal adhesion kinase tyrosine 861 and CUB-domain-containing protein 1 (CDCP1) tyrosine 734.", "journal": "The Journal of biological chemistry", "date": "2011-12-09", "authors": "Wortmann Andreas, He Yaowu, Christensen Melinda E, Linn MayLa, Lumley John W, Pollock Pamela M, Waterhouse Nigel J, Hooper John D", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "21994943", "url": "https://glygen.org/publication/PubMed/21994943" } ] }, { "title": "CUB-domain-containing protein 1 overexpression in solid cancers promotes cancer cell growth by activating Src family kinases.", "journal": "Oncogene", "date": "2015", "authors": "Leroy C, Shen Q, Strande V, Meyer R, McLaughlin ME, Lezan E, Bentires-Alj M, Voshol H, Bonenfant D, Alex Gaither L", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" } ] }, { "title": "The tyrosine phosphatase SHP2 associates with CUB domain-containing protein-1 (CDCP1), regulating its expression at the cell surface in a phosphorylation-dependent manner.", "journal": "PloS one", "date": "2015", "authors": "Gandji LY, Proust R, Larue L, Gesbert F", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044" } ] }, { "title": "Anti-CDCP1 immuno-conjugates for detection and inhibition of ovarian cancer.", "journal": "Theranostics", "date": "2020", "authors": "Harrington Brittney S, He Yaowu, Khan Tashbib, Puttick Simon, Conroy Paul J, Kryza Thomas, Cuda Tahleesa, Sokolowski Kamil A, Tse Brian Wc, Robbins Katherine K, Arachchige Buddhika J, Stehbens Samantha J, Pollock Pamela M, Reed Sarah, Weroha S John, Haluska Paul, Salomon Carlos, Lourie Rohan, Perrin Lewis C, Law Ruby H P, Whisstock James C, Hooper John D", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "32104500", "url": "https://glygen.org/publication/PubMed/32104500" } ] }, { "title": "Effective targeting of intact and proteolysed CDCP1 for imaging and treatment of pancreatic ductal adenocarcinoma.", "journal": "Theranostics", "date": "2020", "authors": "Kryza Thomas, Khan Tashbib, Puttick Simon, Li Chao, Sokolowski Kamil A, Tse Brian Wc, Cuda Tahleesa, Lyons Nicholas, Gough Madeline, Yin Julia, Parkin Ashleigh, Deryugina Elena I, Quigley James P, Law Ruby H P, Whisstock James C, Riddell Andrew D, Barbour Andrew P, Wyld David K, Thomas Paul A, Rose Stephen, Snell Cameron E, Pajic Marina, He Yaowu, Hooper John D", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "32226543", "url": "https://glygen.org/publication/PubMed/32226543" } ] } ], "crossref": [ { "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15851033", "url": "https://glygen.org/publication/PubMed/15851033", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "14739293", "url": "https://glygen.org/publication/PubMed/14739293", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21994943", "url": "https://glygen.org/publication/PubMed/21994943", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32104500", "url": "https://glygen.org/publication/PubMed/32104500", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32226543", "url": "https://glygen.org/publication/PubMed/32226543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EMPRQPKKFQKGRKDNDSHV", "down_seq": "AVIEDTMVYGHLLQDSSGSF", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Impaired association with SRC.", "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" }, { "database": "PubMed", "id": "15851033", "url": "https://glygen.org/publication/PubMed/15851033" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "14739293", "url": "https://glygen.org/publication/PubMed/14739293" } ], "site_lbl": "Tyr734" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" }, { "database": "PubMed", "id": "14739293", "url": "https://glygen.org/publication/PubMed/14739293" }, { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "21994943", "url": "https://glygen.org/publication/PubMed/21994943" }, { "database": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" }, { "database": "PubMed", "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044" }, { "database": "PubMed", "id": "32104500", "url": "https://glygen.org/publication/PubMed/32104500" }, { "database": "PubMed", "id": "32226543", "url": "https://glygen.org/publication/PubMed/32226543" } ], "site_lbl": "Tyr734" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q9H5V8-1.743.743", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9H5V8-1.749.749", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H5V8-1.762.762", "start_pos": 762, "end_pos": 762, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The C2 domain of PKCdelta is a phosphotyrosine binding domain.", "journal": "Cell", "date": "2005", "authors": "Benes CH, Wu N, Elia AE, Dharia T, Cantley LC, Soltoff SP", "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "15851033", "url": "https://glygen.org/publication/PubMed/15851033" } ] }, { "title": "CUB-domain-containing protein 1 overexpression in solid cancers promotes cancer cell growth by activating Src family kinases.", "journal": "Oncogene", "date": "2015", "authors": "Leroy C, Shen Q, Strande V, Meyer R, McLaughlin ME, Lezan E, Bentires-Alj M, Voshol H, Bonenfant D, Alex Gaither L", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" } ] }, { "title": "The tyrosine phosphatase SHP2 associates with CUB domain-containing protein-1 (CDCP1), regulating its expression at the cell surface in a phosphorylation-dependent manner.", "journal": "PloS one", "date": "2015", "authors": "Gandji LY, Proust R, Larue L, Gesbert F", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044" } ] } ], "crossref": [ { "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15851033", "url": "https://glygen.org/publication/PubMed/15851033", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VYGHLLQDSSGSFLQPEVDT", "down_seq": "RPFQGTMGVCPPSPPTICSR", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Impaired association with protein kinase PRKCG but not with SRC.", "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" }, { "database": "PubMed", "id": "15851033", "url": "https://glygen.org/publication/PubMed/15851033" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" }, { "database": "PubMed", "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044" } ], "site_lbl": "Tyr762" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9H5V8-1.743.743", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9H5V8-1.749.749", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "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": "Q9H5V8-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs754445889", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754445889", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754445889", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754445889", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754445889", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754445889#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754445889", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754445889", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs754445889", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754445889", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QIGPGESCPDGVTHSISGRI", "down_seq": "ATVVRIGTFCSNGTVSRIKM", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" }, { "id": "rs754445889", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754445889" }, { "id": "rs754445889", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754445889" }, { "id": "rs754445889", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754445889#frequency_tab" }, { "id": "rs754445889", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754445889" }, { "id": "rs754445889", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754445889" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-gain (DAT->NAT).", "chr_id": "3", "chr_pos": "45112236", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D168", "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", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9H5V8-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9H5V8-1.180.180", "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": "Q9H5V8-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "ELQFSIPRLRQIGPGESCPD", "down_seq": "VTHSISGRIDATVVRIGTFC", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "45112266", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "G158", "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: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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q9H5V8-1.168.168", "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": "Q9H5V8-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1698704300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1698704300", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1698704300", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1698704300#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KMQEGVKMALHLPWFHPRNV", "down_seq": "GFSIANRSSIKRLCIIESVF", "snv": [ { "evidence": [ { "id": "rs1698704300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1698704300" }, { "id": "rs1698704300", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1698704300#frequency_tab" } ], "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 (NVS->NVY).", "chr_id": "3", "chr_pos": "45112118", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S207", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H5V8-1.205.205", "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": "Q9H5V8-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CIIESVFEGEGSATLMSANY", "down_seq": "EGFPEDELMTWQFVVPAHLR", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "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 (NYP->NYS).", "chr_id": "3", "chr_pos": "45110776", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P241", "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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "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": "Q9H5V8-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WQFVVPAHLRASVSFLNFNL", "down_seq": "NCERKEERVEYYIPGSTTNP", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "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 (NLS->NLF).", "chr_id": "3", "chr_pos": "45110682", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S272", "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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H5V8-1.270.270", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9H5V8-1.281.296", "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": "Q9H5V8-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PGSTTNPEVFKLEDKQPGNM", "down_seq": "GNFNLSLQGCDQDAQSPGIL", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NMA->NMT).", "chr_id": "3", "chr_pos": "45110581", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A306", "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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9H5V8-1.281.296", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9H5V8-1.310.310", "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": "Q9H5V8-1.341.341", "start_pos": 341, "end_pos": 341, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs928726101", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs928726101", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs928726101", "url": "https://www.ncbi.nlm.nih.gov/snp/rs928726101#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs928726101", "url": "http://gnomad.broadinstitute.org/awesome?query=rs928726101", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QSPGILRLQFQVLVQHPQNE", "down_seq": "NKIYVVDLSNERAMSLTIEP", "snv": [ { "evidence": [ { "id": "rs928726101", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs928726101" }, { "id": "rs928726101", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs928726101#frequency_tab" }, { "id": "rs928726101", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs928726101" } ], "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 (NES->NEN).", "chr_id": "3", "chr_pos": "45110475", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S341", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H5V8-1.339.339", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9H5V8-1.344.344", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H5V8-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs998187220", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs998187220", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs998187220", "url": "https://www.ensembl.org/id/rs998187220", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "GILRLQFQVLVQHPQNESNK", "down_seq": "YVVDLSNERAMSLTIEPRPV", "snv": [ { "evidence": [ { "id": "rs998187220", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs998187220" }, { "id": "rs998187220", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs998187220" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKI->NKT).", "chr_id": "3", "chr_pos": "45095562", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I344", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9H5V8-1.339.339", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9H5V8-1.341.341", "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": "Q9H5V8-1.388.388", "start_pos": 388, "end_pos": 388, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RKFVPGCFVCLESRTCSSNL", "down_seq": "LTSGSKHKISFLCDDLTRLW", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLA).", "chr_id": "3", "chr_pos": "45095431", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T388", "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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H5V8-1.386.386", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9H5V8-1.396.396", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H5V8-1.396.396", "start_pos": 396, "end_pos": 396, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1325967250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1325967250", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1325967250", "url": "https://www.ensembl.org/id/rs1325967250", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VCLESRTCSSNLTLTSGSKH", "down_seq": "ISFLCDDLTRLWMNVEKTIS", "snv": [ { "evidence": [ { "id": "rs1325967250", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1325967250" }, { "id": "rs1325967250", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1325967250" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KIS->NIS).", "chr_id": "3", "chr_pos": "45095405", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K396", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9H5V8-1.386.386", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9H5V8-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9H5V8-1.416.416", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H5V8-1.416.416", "start_pos": 416, "end_pos": 416, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs758922317", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758922317", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758922317", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758922317", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758922317", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758922317#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758922317", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758922317", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KISFLCDDLTRLWMNVEKTI", "down_seq": "CTDHRYCQRKSYSLQVPSDI", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" }, { "id": "rs758922317", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758922317" }, { "id": "rs758922317", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758922317" }, { "id": "rs758922317", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758922317#frequency_tab" }, { "id": "rs758922317", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758922317" } ], "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 (SCT->NCT).", "chr_id": "3", "chr_pos": "45093657", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S416", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9H5V8-1.396.396", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H5V8-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs370402641", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370402641", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370402641", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370402641", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370402641", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370402641#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs370402641", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370402641", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ARLPRGAEAFEIALPRESNI", "down_seq": "VLIKLGTPTLLAKPCYIVIS", "snv": [ { "evidence": [ { "id": "rs370402641", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370402641" }, { "id": "rs370402641", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370402641" }, { "id": "rs370402641", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370402641#frequency_tab" }, { "id": "rs370402641", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370402641" } ], "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": "3", "chr_pos": "45118582", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T41", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H5V8-1.39.39", "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": "Q9H5V8-1.453.453", "start_pos": 453, "end_pos": 453, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PSDILHLPVELHDFSWKLLV", "down_seq": "KDRLSLVLVPAQKLQQHTHE", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "3", "chr_pos": "45093547", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P453", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "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": "Q9H5V8-1.514.514", "start_pos": 514, "end_pos": 514, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1330961652", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1330961652", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1330961652", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1330961652", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YFGSFCPGGSIKQIQVKQNI", "down_seq": "VTLRTFAPSFQQEASRQGLT", "snv": [ { "evidence": [ { "id": "rs1330961652", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1330961652" }, { "id": "rs1330961652", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1330961652" } ], "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 (NIS->NIL).", "chr_id": "3", "chr_pos": "45093363", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S514", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H5V8-1.512.512", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9H5V8-1.518.518", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H5V8-1.518.518", "start_pos": 518, "end_pos": 518, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FCPGGSIKQIQVKQNISVTL", "down_seq": "TFAPSFQQEASRQGLTVSFI", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "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": "3", "chr_pos": "45093351", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R518", "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: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: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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9H5V8-1.512.512", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9H5V8-1.514.514", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H5V8-1.579.579", "start_pos": 579, "end_pos": 579, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1698294660", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1698294660", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1698294660", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1698294660#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LRTPNWDRGLPSLTSVSWNI", "down_seq": "VPRDQVACLTFFKERSGVVC", "snv": [ { "evidence": [ { "id": "rs1698294660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1698294660" }, { "id": "rs1698294660", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1698294660#frequency_tab" } ], "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 (NIS->NII).", "chr_id": "3", "chr_pos": "45091430", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S579", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H5V8-1.577.577", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9H5V8-1.589.589", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H5V8-1.589.589", "start_pos": 589, "end_pos": 589, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSLTSVSWNISVPRDQVACL", "down_seq": "FFKERSGVVCQTGRAFMIIQ", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "T", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "3", "chr_pos": "45091401", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T589", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9H5V8-1.577.577", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9H5V8-1.579.579", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9H5V8-1.601.601", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9H5V8-1.604.604", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q9H5V8-1.604.604", "start_pos": 604, "end_pos": 604, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QVACLTFFKERSGVVCQTGR", "down_seq": "FMIIQEQRTRAEEIFSLDED", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "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 (4).", "chr_id": "3", "chr_pos": "45091356", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A604", "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: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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9H5V8-1.589.589", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9H5V8-1.601.601", "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": "Q9H5V8-1.696.696", "start_pos": 696, "end_pos": 696, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1576071877", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1576071877", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1576071877", "url": "https://www.ensembl.org/id/rs1576071877", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GGVLLLSALGLIICCVKKKK", "down_seq": "KTNKGPAVGIYNDNINTEMP", "snv": [ { "evidence": [ { "id": "rs1576071877", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1576071877" }, { "id": "rs1576071877", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1576071877" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KKT->NKT).", "chr_id": "3", "chr_pos": "45086061", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K696", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q9H5V8-1.707.707", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9H5V8-1.710.710", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H5V8-1.710.710", "start_pos": 710, "end_pos": 710, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772792426", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772792426", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772792426", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772792426", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772792426", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772792426", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CVKKKKKKTNKGPAVGIYND", "down_seq": "INTEMPRQPKKFQKGRKDND", "snv": [ { "evidence": [ { "id": "rs772792426", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772792426" }, { "id": "rs772792426", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772792426" }, { "id": "rs772792426", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772792426" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDN->NDT).", "chr_id": "3", "chr_pos": "45086020", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N710", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9H5V8-1.696.696", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9H5V8-1.707.707", "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": "Q9H5V8-1.749.749", "start_pos": 749, "end_pos": 749, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs141086872", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141086872", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs141086872", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141086872", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs141086872", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141086872", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs141086872", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141086872#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs141086872", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141086872", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NDSHVYAVIEDTMVYGHLLQ", "down_seq": "SSGSFLQPEVDTYRPFQGTM", "snv": [ { "evidence": [ { "id": "rs141086872", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141086872" }, { "id": "rs141086872", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141086872" }, { "id": "rs141086872", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141086872" }, { "id": "rs141086872", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141086872#frequency_tab" }, { "id": "rs141086872", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141086872" } ], "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": "3", "chr_pos": "45085904", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "D749", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9H5V8-1.734.734", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9H5V8-1.743.743", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9H5V8-1.762.762", "categories": [ "mutagenesis_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": "Q9H5V8-1.819.819", "start_pos": 819, "end_pos": 819, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H5V8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PESESEPYTFSHPNNGDVSS", "down_seq": "DTDIPLLNTQEPMEPAE", "snv": [ { "evidence": [ { "id": "Q9H5V8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H5V8" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KDT->NDT).", "chr_id": "3", "chr_pos": "45085692", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K819", "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": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9H5V8-1.803.803", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9H5V8-1.806.806", "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": "Q9H5V8-1.601.601", "start_pos": 601, "end_pos": 601, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q9H5V8", "url": "https://www.iedb.org/epitope/Q9H5V8", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8", "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": "PRDQVACLTFFKERSGVVCQ", "down_seq": "GRAFMIIQEQRTRAEEIFSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q9H5V8", "url": "https://www.iedb.org/epitope/Q9H5V8" }, { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr601" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9H5V8-1.589.589", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9H5V8-1.604.604", "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": "Q9H5V8-1.707.707", "start_pos": 707, "end_pos": 707, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "CUB-domain-containing protein 1 overexpression in solid cancers promotes cancer cell growth by activating Src family kinases.", "journal": "Oncogene", "date": "2015", "authors": "Leroy C, Shen Q, Strande V, Meyer R, McLaughlin ME, Lezan E, Bentires-Alj M, Voshol H, Bonenfant D, Alex Gaither L", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" } ] } ], "crossref": [ { "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IICCVKKKKKKTNKGPAVGI", "down_seq": "NDNINTEMPRQPKKFQKGRK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" } ], "site_lbl": "Tyr707" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9H5V8-1.696.696", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9H5V8-1.710.710", "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": "Q9H5V8-1.743.743", "start_pos": 743, "end_pos": 743, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "CUB-domain-containing protein 1 overexpression in solid cancers promotes cancer cell growth by activating Src family kinases.", "journal": "Oncogene", "date": "2015", "authors": "Leroy C, Shen Q, Strande V, Meyer R, McLaughlin ME, Lezan E, Bentires-Alj M, Voshol H, Bonenfant D, Alex Gaither L", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" } ] }, { "title": "The tyrosine phosphatase SHP2 associates with CUB domain-containing protein-1 (CDCP1), regulating its expression at the cell surface in a phosphorylation-dependent manner.", "journal": "PloS one", "date": "2015", "authors": "Gandji LY, Proust R, Larue L, Gesbert F", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044" } ] } ], "crossref": [ { "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QKGRKDNDSHVYAVIEDTMV", "down_seq": "GHLLQDSSGSFLQPEVDTYR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" }, { "database": "PubMed", "id": "25876044", "url": "https://glygen.org/publication/PubMed/25876044" } ], "site_lbl": "Tyr743" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9H5V8-1.734.734", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9H5V8-1.749.749", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9H5V8-1.762.762", "categories": [ "mutagenesis_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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H5V8-1.797.797", "start_pos": 797, "end_pos": 797, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "Q9H5V8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8", "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": "PTICSRAPTAKLATEEPPPR", "down_seq": "PPESESEPYTFSHPNNGDVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser797" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9H5V8-1.803.803", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9H5V8-1.806.806", "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": "Q9H5V8-1.803.803", "start_pos": 803, "end_pos": 803, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "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": "Q9H5V8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8", "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": "APTAKLATEEPPPRSPPESE", "down_seq": "EPYTFSHPNNGDVSSKDTDI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser803" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9H5V8-1.797.797", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9H5V8-1.806.806", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9H5V8-1.819.819", "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": "Q9H5V8-1.806.806", "start_pos": 806, "end_pos": 806, "uniprot_canonical_ac": "Q9H5V8-1", "length": 836, "uniprot_id": "CDCP1_HUMAN", "protein_name": "CUB domain-containing protein 1", "refseq_ac": "NP_073753", "refseq_name": "CUB domain-containing protein 1 isoform 1 precursor", "gene_name": "CDCP1", "gene_names_uniprotkb": "CDCP1; PRO5773; TRASK", "gene_names_refseq": "CD318; CDCP1; SIMA135; TRASK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H5V8", "url": "https://www.uniprot.org/uniprotkb/Q9H5V8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "CUB-domain-containing protein 1 overexpression in solid cancers promotes cancer cell growth by activating Src family kinases.", "journal": "Oncogene", "date": "2015", "authors": "Leroy C, Shen Q, Strande V, Meyer R, McLaughlin ME, Lezan E, Bentires-Alj M, Voshol H, Bonenfant D, Alex Gaither L", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" } ], "reference": [ { "type": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" } ] } ], "crossref": [ { "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AKLATEEPPPRSPPESESEP", "down_seq": "TFSHPNNGDVSSKDTDIPLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H5V8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H5V8" }, { "database": "PubMed", "id": "25728678", "url": "https://glygen.org/publication/PubMed/25728678" } ], "site_lbl": "Tyr806" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "281", "end_pos": "296" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "577", "end_pos": "577" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "734", "end_pos": "734" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "589", "end_pos": "589" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "696", "end_pos": "696" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "819", "end_pos": "819" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "601", "end_pos": "601" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "734", "end_pos": "734" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "803", "end_pos": "803" }, { "start_pos": "806", "end_pos": "806" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9H5V8-1.797.797", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9H5V8-1.803.803", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9H5V8-1.819.819", "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": "Q9NP86-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "Q9NP86-1", "length": 173, "uniprot_id": "CABP5_HUMAN", "protein_name": "Calcium-binding protein 5", "refseq_ac": "NP_062829", "refseq_name": "calcium-binding protein 5", "gene_name": "CABP5", "gene_names_uniprotkb": "CABP5; CABP3", "gene_names_refseq": "CABP3; CABP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NP86", "url": "https://www.uniprot.org/uniprotkb/Q9NP86" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NP86", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NP86", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "VDFDDFVELMTPKLLAETAG", "down_seq": "IGVQEMRDAFKEFDTNGDGE", "snv": [ { "evidence": [ { "id": "Q9NP86", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NP86" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "48039244", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M104", "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: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": "104", "end_pos": "104" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "83", "end_pos": "83" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q9NP86-1.111.111", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NP86-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "Q9NP86-1", "length": 173, "uniprot_id": "CABP5_HUMAN", "protein_name": "Calcium-binding protein 5", "refseq_ac": "NP_062829", "refseq_name": "calcium-binding protein 5", "gene_name": "CABP5", "gene_names_uniprotkb": "CABP5; CABP3", "gene_names_refseq": "CABP3; CABP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NP86", "url": "https://www.uniprot.org/uniprotkb/Q9NP86" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NP86", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NP86", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELMTPKLLAETAGMIGVQEM", "down_seq": "DAFKEFDTNGDGEITLVELQ", "snv": [ { "evidence": [ { "id": "Q9NP86", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NP86" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "19", "chr_pos": "48039225", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R111", "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: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": "104", "end_pos": "104" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "83", "end_pos": "83" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9NP86-1.104.104", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NP86-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "Q9NP86-1", "length": 173, "uniprot_id": "CABP5_HUMAN", "protein_name": "Calcium-binding protein 5", "refseq_ac": "NP_062829", "refseq_name": "calcium-binding protein 5", "gene_name": "CABP5", "gene_names_uniprotkb": "CABP5; CABP3", "gene_names_refseq": "CABP3; CABP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NP86", "url": "https://www.uniprot.org/uniprotkb/Q9NP86" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NP86", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NP86", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MPTEMELIELGQQIRMNLGG", "down_seq": "VDFDDFVELMTPKLLAETAG", "snv": [ { "evidence": [ { "id": "Q9NP86", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NP86" } ], "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": "19", "chr_pos": "48039308", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R83", "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: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": "104", "end_pos": "104" }, { "start_pos": "111", "end_pos": "111" }, { "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NTU7-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "journal": "Analytical chemistry", "date": "2018", "authors": "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "2027", "url": "https://glyconnect.expasy.org/browser/proteins/2027" } ], "reference": [ { "type": "PubMed", "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580" } ] } ], "crossref": [ { "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "2027", "url": "https://glyconnect.expasy.org/browser/proteins/2027", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "PRU00498", "url": "https://prosite.expasy.org/rule/PRU00498", "database": "PROSITE-ProRule", "categories": [ "Other" ] }, { "id": "rs905118183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs905118183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs905118183", "url": "http://gnomad.broadinstitute.org/awesome?query=rs905118183", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SAVPAVLLVLTLPGLPVWAQ", "down_seq": "DTEPIVLEGKCLVVCDSNPA", "glycosylation": [ { "glytoucan_ac": "G06247RL", "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": "Asn29", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "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": "Asn29", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "2027", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2027" } ] }, { "glytoucan_ac": "G47518TP", "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": "Asn29", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "2027", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2027" } ] }, { "glytoucan_ac": "G94917XT", "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": "Asn29", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "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": "Asn29", "evidence": [ { "id": "Q9NTU7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7#ptm_processing" }, { "id": "PRU00498", "database": "PROSITE-ProRule", "url": "https://prosite.expasy.org/rule/PRU00498" } ] } ], "snv": [ { "evidence": [ { "id": "rs905118183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs905118183" }, { "id": "rs905118183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs905118183" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDT->KDT).", "chr_id": "20", "chr_pos": "56004085", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N29", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9NTU7-1.31.31", "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" ] }, { "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": 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": "Q9NTU7-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "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": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "PRU00498", "url": "https://prosite.expasy.org/rule/PRU00498", "database": "PROSITE-ProRule", "categories": [ "Other" ] }, { "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" ] }, { "id": "rs919581174", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs919581174", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs919581174", "url": "https://www.ncbi.nlm.nih.gov/snp/rs919581174#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs919581174", "url": "http://gnomad.broadinstitute.org/awesome?query=rs919581174", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NSKVAFSAVRSTNHEPSEMS", "down_seq": "KTRIIYFDQILVNVGNFFTL", "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": "Asn88", "evidence": [ { "id": "Q9NTU7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7#ptm_processing" }, { "id": "PRU00498", "database": "PROSITE-ProRule", "url": "https://prosite.expasy.org/rule/PRU00498" }, { "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" } ] } ], "snv": [ { "evidence": [ { "id": "rs919581174", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs919581174" }, { "id": "rs919581174", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs919581174#frequency_tab" }, { "id": "rs919581174", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs919581174" } ], "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": "56003908", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N88", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9NTU7-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9NTU7-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9NTU7-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9NTU7-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9NTU7-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9NTU7-1.106.106", "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": 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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q9NTU7-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1187097675", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1187097675", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1187097675", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1187097675#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1187097675", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1187097675", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PSEMSNKTRIIYFDQILVNV", "down_seq": "NFFTLESVFVAPRKGIYSFS", "snv": [ { "evidence": [ { "id": "rs1187097675", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1187097675" }, { "id": "rs1187097675", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1187097675#frequency_tab" }, { "id": "rs1187097675", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1187097675" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVG->NVC).", "chr_id": "20", "chr_pos": "56000832", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G103", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9NTU7-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9NTU7-1.88.88", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9NTU7-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9NTU7-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9NTU7-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9NTU7-1.121.121", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NTU7-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NTU7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MSNKTRIIYFDQILVNVGNF", "down_seq": "TLESVFVAPRKGIYSFSFHV", "snv": [ { "evidence": [ { "id": "Q9NTU7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NFF->NFS).", "chr_id": "20", "chr_pos": "56000822", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "F106", "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": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9NTU7-1.88.88", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9NTU7-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9NTU7-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9NTU7-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9NTU7-1.121.121", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NTU7-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NTU7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NVGNFFTLESVFVAPRKGIY", "down_seq": "FSFHVIKVYQSQTIQVNLML", "snv": [ { "evidence": [ { "id": "Q9NTU7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SFS->NFS).", "chr_id": "20", "chr_pos": "56000777", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S121", "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": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9NTU7-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9NTU7-1.106.106", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NTU7-1.151.151", "start_pos": 151, "end_pos": 151, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NTU7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QSQTIQVNLMLNGKPVISAF", "down_seq": "GDKDVTREAATNGVLLYLDK", "snv": [ { "evidence": [ { "id": "Q9NTU7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "55998711", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A151", "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: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": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "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": "Q9NTU7-1.31.31", "start_pos": 31, "end_pos": 31, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756594633", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756594633", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756594633", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756594633", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756594633", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756594633", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VPAVLLVLTLPGLPVWAQND", "down_seq": "EPIVLEGKCLVVCDSNPATD", "snv": [ { "evidence": [ { "id": "rs756594633", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756594633" }, { "id": "rs756594633", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756594633" }, { "id": "rs756594633", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756594633" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDT->NDM).", "chr_id": "20", "chr_pos": "56004080", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T31", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9NTU7-1.29.29", "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": "Q9NTU7-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NTU7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VCDSNPATDSKGSSSSPLGI", "down_seq": "VRAANSKVAFSAVRSTNHEP", "snv": [ { "evidence": [ { "id": "Q9NTU7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7" } ], "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 (3).", "chr_id": "20", "chr_pos": "56003984", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S63", "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": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q9NTU7-1.72.72", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NTU7-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NTU7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SKGSSSSPLGISVRAANSKV", "down_seq": "FSAVRSTNHEPSEMSNKTRI", "snv": [ { "evidence": [ { "id": "Q9NTU7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "20", "chr_pos": "56003958", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A72", "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: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: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": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9NTU7-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9NTU7-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9NTU7-1.88.88", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9NTU7-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9NTU7-1.91.91", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NTU7-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NTU7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RAANSKVAFSAVRSTNHEPS", "down_seq": "MSNKTRIIYFDQILVNVGNF", "snv": [ { "evidence": [ { "id": "Q9NTU7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7" } ], "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": "20", "chr_pos": "56003919", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E85", "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: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": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9NTU7-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9NTU7-1.88.88", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9NTU7-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9NTU7-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9NTU7-1.103.103", "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": "Q9NTU7-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764966249", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764966249", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764966249", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764966249", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764966249", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764966249", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9NTU7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KVAFSAVRSTNHEPSEMSNK", "down_seq": "RIIYFDQILVNVGNFFTLES", "snv": [ { "evidence": [ { "id": "rs764966249", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764966249" }, { "id": "rs764966249", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764966249" }, { "id": "rs764966249", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764966249" } ], "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 (NKT->NKK).", "chr_id": "20", "chr_pos": "56003903", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T90", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9NTU7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKT->NKM).", "chr_id": "20", "chr_pos": "56003903", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T90", "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": "rs764966249", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764966249" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->NKR).", "chr_id": "20", "chr_pos": "56003903", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T90", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9NTU7-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9NTU7-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9NTU7-1.88.88", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9NTU7-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9NTU7-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9NTU7-1.106.106", "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": 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": "Q9NTU7-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q9NTU7-1", "length": 201, "uniprot_id": "CBLN4_HUMAN", "protein_name": "Cerebellin-4", "refseq_ac": "NP_542184", "refseq_name": "cerebellin-4 precursor", "gene_name": "CBLN4", "gene_names_uniprotkb": "CBLN4; CBLNL1; PRO1382", "gene_names_refseq": "CBLN4; CBLNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NTU7", "url": "https://www.uniprot.org/uniprotkb/Q9NTU7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NTU7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VAFSAVRSTNHEPSEMSNKT", "down_seq": "IIYFDQILVNVGNFFTLESV", "snv": [ { "evidence": [ { "id": "Q9NTU7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NTU7" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "56003901", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R91", "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": "29", "end_pos": "29" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9NTU7-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9NTU7-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9NTU7-1.88.88", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9NTU7-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9NTU7-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9NTU7-1.106.106", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NUG4-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9NUG4-1", "length": 571, "uniprot_id": "CCM2L_HUMAN", "protein_name": "Cerebral cavernous malformations 2 protein-like", "refseq_ac": "NP_542192", "refseq_name": "cerebral cavernous malformations 2 protein-like isoform 2", "gene_name": "CCM2L", "gene_names_uniprotkb": "CCM2L; C20orf160", "gene_names_refseq": "C20orf160; CCM2L; dJ310O13.5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NUG4", "url": "https://www.uniprot.org/uniprotkb/Q9NUG4" } ], "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": "Q9NUG4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NUG4" } ], "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": "Q9NUG4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NUG4", "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": "Q9NUG4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NUG4" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "36", "end_pos": "36" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q9NUG4-1.17.17", "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": "Q9NUG4-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "Q9NUG4-1", "length": 571, "uniprot_id": "CCM2L_HUMAN", "protein_name": "Cerebral cavernous malformations 2 protein-like", "refseq_ac": "NP_542192", "refseq_name": "cerebral cavernous malformations 2 protein-like isoform 2", "gene_name": "CCM2L", "gene_names_uniprotkb": "CCM2L; C20orf160", "gene_names_refseq": "C20orf160; CCM2L; dJ310O13.5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NUG4", "url": "https://www.uniprot.org/uniprotkb/Q9NUG4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NUG4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NUG4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MEYEVKKGKKGFVSPI", "down_seq": "RLVFPKAGRRAACRSSVSRR", "snv": [ { "evidence": [ { "id": "Q9NUG4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NUG4" } ], "glycoeffect": [], "subjects_tested": "3601", "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": "32014923", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R17", "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: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": "17", "end_pos": "17" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "36", "end_pos": "36" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9NUG4-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9NUG4-1.36.36", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NUG4-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q9NUG4-1", "length": 571, "uniprot_id": "CCM2L_HUMAN", "protein_name": "Cerebral cavernous malformations 2 protein-like", "refseq_ac": "NP_542192", "refseq_name": "cerebral cavernous malformations 2 protein-like isoform 2", "gene_name": "CCM2L", "gene_names_uniprotkb": "CCM2L; C20orf160", "gene_names_refseq": "C20orf160; CCM2L; dJ310O13.5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NUG4", "url": "https://www.uniprot.org/uniprotkb/Q9NUG4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NUG4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NUG4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AYCNLVILAVANRDAAEESC", "down_seq": "LICQVFQIIYGDQSIECVDR", "snv": [ { "evidence": [ { "id": "Q9NUG4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NUG4" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "20", "chr_pos": "32022681", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A319", "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: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": "17", "end_pos": "17" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "36", "end_pos": "36" } ] } ], "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": "Q9NUG4-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "Q9NUG4-1", "length": 571, "uniprot_id": "CCM2L_HUMAN", "protein_name": "Cerebral cavernous malformations 2 protein-like", "refseq_ac": "NP_542192", "refseq_name": "cerebral cavernous malformations 2 protein-like isoform 2", "gene_name": "CCM2L", "gene_names_uniprotkb": "CCM2L; C20orf160", "gene_names_refseq": "C20orf160; CCM2L; dJ310O13.5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NUG4", "url": "https://www.uniprot.org/uniprotkb/Q9NUG4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NUG4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NUG4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IRRLVFPKAGRRAACRSSVS", "down_seq": "RPLHSMPLYPPDYLIDPQIL", "snv": [ { "evidence": [ { "id": "Q9NUG4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NUG4" } ], "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": "32014980", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R36", "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": "17", "end_pos": "17" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "36", "end_pos": "36" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9NUG4-1.17.17", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.428.428", "start_pos": 428, "end_pos": 428, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "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": "Q9UFE4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UFE4" }, { "database": "O-GlcNAc Atlas", "id": "Q9UFE4", "url": "https://oglcnac.org/atlas/detail/Q9UFE4" } ], "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": "Q9UFE4", "url": "https://oglcnac.org/atlas/detail/Q9UFE4", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELQTETMKEKAVLSEIEGTR", "down_seq": "SLKHLNHQLQKLDFETLKQQ", "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": "Ser428", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q9UFE4", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9UFE4" } ] } ], "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "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": "3", "chr_pos": "180648244", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S428", "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": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2003", "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": "3", "chr_pos": "180648244", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S428", "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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9UFE4-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9UFE4-1.422.422", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9UFE4-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9UFE4-1.429.429", "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": 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": "Q9UFE4-1.429.429", "start_pos": 429, "end_pos": 429, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "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": "Q9UFE4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UFE4" }, { "database": "O-GlcNAc Atlas", "id": "Q9UFE4", "url": "https://oglcnac.org/atlas/detail/Q9UFE4" } ], "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": "Q9UFE4", "url": "https://oglcnac.org/atlas/detail/Q9UFE4", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1718118928", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1718118928", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1718118928", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1718118928#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1718118928", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1718118928", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1718118993", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1718118993", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1718118993", "url": "https://www.ensembl.org/id/rs1718118993", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQTETMKEKAVLSEIEGTRS", "down_seq": "LKHLNHQLQKLDFETLKQQE", "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": "Ser429", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q9UFE4", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9UFE4" } ] } ], "snv": [ { "evidence": [ { "id": "rs1718118928", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1718118928" }, { "id": "rs1718118928", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1718118928#frequency_tab" }, { "id": "rs1718118928", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1718118928" } ], "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": "3", "chr_pos": "180648241", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S429", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1718118993", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1718118993" }, { "id": "rs1718118993", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1718118993" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "3", "chr_pos": "180648242", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S429", "disease": [ { "disease_id": "DOID:0110598", "recommended_name": { "id": "DOID:0110598", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110598", "name": "primary ciliary dyskinesia 14", "description": "A primary ciliary dyskinesia that is characterized by autosomal recessive inheritance with inner dynein arm defect and axonemal disorganization, chronic upper and lower airway infections, and has_material_basis_in homozygous or compound heterozygous mutation in the CCDC39 gene on chromosome 3q26." }, "synonyms": [ { "id": "DOID:0110598", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110598", "name": "CILD14", "description": "" }, { "id": "DOID:0110598", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110598", "name": "primary ciliary dyskinesia 14 with or without situs inversus", "description": "" }, { "id": "MONDO:0013434", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013434", "name": "primary ciliary dyskinesia 14", "description": "Any primary ciliary dyskinesia in which the cause of the disease is a mutation in the CCDC39 gene." }, { "id": "MONDO:0013434", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013434", "name": "CCDC39 primary ciliary dyskinesia", "description": "" }, { "id": "MONDO:0013434", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013434", "name": "CILD14", "description": "" }, { "id": "MONDO:0013434", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013434", "name": "ciliary dyskinesia, primary, type 14", "description": "" }, { "id": "MONDO:0013434", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013434", "name": "primary ciliary dyskinesia 14", "description": "" }, { "id": "MONDO:0013434", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013434", "name": "primary ciliary dyskinesia caused by mutation in CCDC39", "description": "" }, { "id": "MONDO:0013434", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013434", "name": "primary ciliary dyskinesia type 14", "description": "" }, { "id": "MONDO:0013434", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013434", "name": "ciliary dyskinesia, primary, 14", "description": "" }, { "id": "MIM:613807", "resource": "MIM", "url": "https://www.omim.org/entry/613807", "name": "Ciliary dyskinesia, primary, 14", "description": "Ciliary dyskinesia, primary, 14" } ], "unlinked_id_list": [], "evidence": [ { "id": "613807", "database": "MIM", "url": "https://www.omim.org/entry/613807" }, { "id": "0110598", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0110598" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9UFE4-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9UFE4-1.422.422", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UFE4-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9UFE4-1.428.428", "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": [ "sequence_org", "sequence_mut", "comment", "chr_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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9UFE4-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "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": "Q9UFE4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UFE4" }, { "database": "O-GlcNAc Atlas", "id": "Q9UFE4", "url": "https://oglcnac.org/atlas/detail/Q9UFE4" } ], "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": "Q9UFE4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UFE4", "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": "Q9UFE4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UFE4" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EEHFKAIAQRELGRVKDEIQ", "down_seq": "LENEMASILEKKSDKENGIF", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "180661911", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R103", "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: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: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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9UFE4-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9UFE4-1.114.114", "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": "Q9UFE4-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773453297", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773453297", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773453297", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773453297", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773453297", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773453297", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "AIAQRELGRVKDEIQRLENE", "down_seq": "ASILEKKSDKENGIFKATQK", "snv": [ { "evidence": [ { "id": "rs773453297", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773453297" }, { "id": "rs773453297", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773453297" }, { "id": "rs773453297", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773453297" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEM->NET).", "chr_id": "3", "chr_pos": "180661895", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M108", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9UFE4-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9UFE4-1.114.114", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LGRVKDEIQRLENEMASILE", "down_seq": "KSDKENGIFKATQKLDGLKC", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KKS->NKS).", "chr_id": "3", "chr_pos": "180661876", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K114", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9UFE4-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9UFE4-1.108.108", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ATQKLDGLKCQMNWDQQALE", "down_seq": "WLEESAHKDSDALTLQKYAQ", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "180660652", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A145", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs983121717", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs983121717", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs983121717", "url": "https://www.ensembl.org/id/rs983121717", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "AHKDSDALTLQKYAQQDDNK", "down_seq": "RALTLQLERLTLECNQKRKI", "snv": [ { "evidence": [ { "id": "rs983121717", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs983121717" }, { "id": "rs983121717", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs983121717" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKI->NKT).", "chr_id": "3", "chr_pos": "180660574", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I171", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q9UFE4-1.184.184", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AQQDDNKIRALTLQLERLTL", "down_seq": "CNQKRKILDNELTETISAQL", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "180659736", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E184", "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: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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9UFE4-1.171.171", "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": "Q9UFE4-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NELTETISAQLELDKAAQDF", "down_seq": "KIHNERQELIKQWENTIEQM", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "12", "frequency": "0.6", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: patient count (12/2053).", "chr_id": "3", "chr_pos": "180659550", "ref_nt": "G", "alt_nt": "A", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9UFE4-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9UFE4-1.231.231", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AQLELDKAAQDFRKIHNERQ", "down_seq": "LIKQWENTIEQMQKRDGDID", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "180659526", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E222", "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" } ] }, { "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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9UFE4-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9UFE4-1.231.231", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748172583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748172583", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748172583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748172583", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748172583", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748172583#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748172583", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748172583", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "QDFRKIHNERQELIKQWENT", "down_seq": "EQMQKRDGDIDNCALELARI", "snv": [ { "evidence": [ { "id": "rs748172583", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748172583" }, { "id": "rs748172583", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748172583" }, { "id": "rs748172583", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748172583#frequency_tab" }, { "id": "rs748172583", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748172583" } ], "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": "3", "chr_pos": "180659498", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I231", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9UFE4-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9UFE4-1.222.222", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ALELARIKQETREKENLVKE", "down_seq": "IKFLESEIGNNTEFEKRISV", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "180654897", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K265", "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: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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NNTEFEKRISVADRKLLKCR", "down_seq": "AYQDHETSRIQLKGELDSLK", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "3", "chr_pos": "180654808", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T295", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9UFE4-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9UFE4-1.315.315", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q9UFE4-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1236397924", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1236397924", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1236397924", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1236397924#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1236397924", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1236397924", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "EKRISVADRKLLKCRTAYQD", "down_seq": "ETSRIQLKGELDSLKATVNR", "snv": [ { "evidence": [ { "id": "rs1236397924", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1236397924" }, { "id": "rs1236397924", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1236397924#frequency_tab" }, { "id": "rs1236397924", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1236397924" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HET->NET).", "chr_id": "3", "chr_pos": "180654794", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H300", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9UFE4-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9UFE4-1.315.315", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1234465832", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1234465832", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1234465832", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1234465832", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TAYQDHETSRIQLKGELDSL", "down_seq": "ATVNRTSSDLEALRKNISKI", "snv": [ { "evidence": [ { "id": "rs1234465832", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1234465832" }, { "id": "rs1234465832", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1234465832" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAT->NAT).", "chr_id": "3", "chr_pos": "180652252", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K315", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9UFE4-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9UFE4-1.300.300", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NEIIQTKLKEITEKTMSVEE", "down_seq": "ATNLEDMLKEEEKDVKEVDV", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "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 (KAT->NAT).", "chr_id": "3", "chr_pos": "180651449", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K373", "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: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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.411.411", "start_pos": 411, "end_pos": 411, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VDVQLNLIKGVLFKKAQELQ", "down_seq": "ETMKEKAVLSEIEGTRSSLK", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TET->NET).", "chr_id": "3", "chr_pos": "180648295", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T411", "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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q9UFE4-1.422.422", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9UFE4-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9UFE4-1.428.428", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9UFE4-1.429.429", "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": "Q9UFE4-1.422.422", "start_pos": 422, "end_pos": 422, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LFKKAQELQTETMKEKAVLS", "down_seq": "IEGTRSSLKHLNHQLQKLDF", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "3", "chr_pos": "180648263", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E422", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9UFE4-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9UFE4-1.427.427", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9UFE4-1.428.428", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9UFE4-1.429.429", "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": "Q9UFE4-1.427.427", "start_pos": 427, "end_pos": 427, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QELQTETMKEKAVLSEIEGT", "down_seq": "SSLKHLNHQLQKLDFETLKQ", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "180648247", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R427", "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: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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9UFE4-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9UFE4-1.422.422", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9UFE4-1.428.428", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UFE4-1.429.429", "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": "Q9UFE4-1.463.463", "start_pos": 463, "end_pos": 463, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ETLKQQEIMYSQDFHIQQVE", "down_seq": "RMSRLKGEINSEEKQALEAK", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "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": "3", "chr_pos": "180647219", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R463", "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: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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q9UFE4-1.479.479", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.479.479", "start_pos": 479, "end_pos": 479, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QQVERRMSRLKGEINSEEKQ", "down_seq": "LEAKIVELRKSLEEKKSTCG", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "180647170", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A479", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9UFE4-1.463.463", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LSKLKDERASLQDELREYEE", "down_seq": "INSMTSHFKNVKQELSITQS", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "180663925", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R51", "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": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q9UFE4-1.55.55", "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": "Q9UFE4-1.526.526", "start_pos": 526, "end_pos": 526, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1192316779", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1192316779", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1192316779", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1192316779#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1192316779", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1192316779", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KKLHNDLYFIKKAHSKNSDE", "down_seq": "QSLMTKINELNLFIDRSEKE", "snv": [ { "evidence": [ { "id": "rs1192316779", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1192316779" }, { "id": "rs1192316779", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1192316779#frequency_tab" }, { "id": "rs1192316779", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1192316779" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KQS->NQS).", "chr_id": "3", "chr_pos": "180644207", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K526", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q9UFE4-1.541.541", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.541.541", "start_pos": 541, "end_pos": 541, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764908281", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764908281", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764908281", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764908281", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764908281", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764908281#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764908281", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764908281", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KNSDEKQSLMTKINELNLFI", "down_seq": "RSEKELDKAKGFKQDLMIED", "snv": [ { "evidence": [ { "id": "rs764908281", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764908281" }, { "id": "rs764908281", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764908281" }, { "id": "rs764908281", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764908281#frequency_tab" }, { "id": "rs764908281", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764908281" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DRS->NRS).", "chr_id": "3", "chr_pos": "180644164", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D541", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9UFE4-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9UFE4-1.547.547", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.547.547", "start_pos": 547, "end_pos": 547, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "QSLMTKINELNLFIDRSEKE", "down_seq": "DKAKGFKQDLMIEDNLLKLE", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "180644145", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L547", "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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9UFE4-1.541.541", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1560093308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1560093308", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1560093308", "url": "https://www.ensembl.org/id/rs1560093308", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "KDERASLQDELREYEERINS", "down_seq": "TSHFKNVKQELSITQSLCKA", "snv": [ { "evidence": [ { "id": "rs1560093308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1560093308" }, { "id": "rs1560093308", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1560093308" } ], "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": "3", "chr_pos": "180663913", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M55", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q9UFE4-1.51.51", "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": "Q9UFE4-1.570.570", "start_pos": 570, "end_pos": 570, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AKGFKQDLMIEDNLLKLEVK", "down_seq": "TREMLHSKAEEVLSLEKRKQ", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "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": "3", "chr_pos": "180642158", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R570", "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: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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.642.642", "start_pos": 642, "end_pos": 642, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779876609", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779876609", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779876609", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779876609", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779876609", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779876609", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ENISTEFRERLSKIEKLKNR", "down_seq": "EILTVVMLPPEGEEEKTQAY", "snv": [ { "evidence": [ { "id": "rs779876609", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779876609" }, { "id": "rs779876609", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779876609" }, { "id": "rs779876609", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779876609" } ], "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 (NRY->NRC).", "chr_id": "3", "chr_pos": "180631542", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y642", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.694.694", "start_pos": 694, "end_pos": 694, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LQREGDCLDAKINKAEKEIY", "down_seq": "LENTLQVLNSCNNNYKQSFK", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "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": "3", "chr_pos": "180619889", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A694", "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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.728.728", "start_pos": 728, "end_pos": 728, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "NYKQSFKKVTPSSDEYELKI", "down_seq": "LEEQKRAVDEKYRYKQRQIR", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "3", "chr_pos": "180619340", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q728", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.787.787", "start_pos": 787, "end_pos": 787, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LANNVKEKLSEKQAYSFQLS", "down_seq": "ETEEQKPKLERVTKQCAKLT", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KET->NET).", "chr_id": "3", "chr_pos": "180616871", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K787", "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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.876.876", "start_pos": 876, "end_pos": 876, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LQTYFQQSGLELPTASTKGS", "down_seq": "QSSRSPSHTSLSARSSRSTS", "snv": [ { "evidence": [ { "id": "Q9UFE4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UFE4" } ], "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 (5).", "chr_id": "3", "chr_pos": "180616324", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R876", "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: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": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9UFE4-1.884.884", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9UFE4-1.892.892", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9UFE4-1.894.894", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9UFE4-1.896.896", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UFE4-1.884.884", "start_pos": 884, "end_pos": 884, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1245757928", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245757928", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1245757928", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1245757928", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GLELPTASTKGSRQSSRSPS", "down_seq": "TSLSARSSRSTSTSTSQSSI", "snv": [ { "evidence": [ { "id": "rs1245757928", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245757928" }, { "id": "rs1245757928", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1245757928" } ], "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": "3", "chr_pos": "180616300", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H884", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9UFE4-1.876.876", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9UFE4-1.892.892", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9UFE4-1.894.894", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9UFE4-1.896.896", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9UFE4-1.900.900", "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": "Q9UFE4-1.894.894", "start_pos": 894, "end_pos": 894, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1302714959", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1302714959", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1302714959", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1302714959", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSRQSSRSPSHTSLSARSSR", "down_seq": "TSTSTSQSSIKVLELKFPAS", "snv": [ { "evidence": [ { "id": "rs1302714959", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1302714959" }, { "id": "rs1302714959", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1302714959" } ], "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 (STS->NTS).", "chr_id": "3", "chr_pos": "180615066", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S894", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9UFE4-1.876.876", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9UFE4-1.884.884", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UFE4-1.892.892", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UFE4-1.896.896", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9UFE4-1.900.900", "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": "Q9UFE4-1.896.896", "start_pos": 896, "end_pos": 896, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1386857992", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386857992", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1386857992", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386857992", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQSSRSPSHTSLSARSSRST", "down_seq": "TSTSQSSIKVLELKFPASSS", "snv": [ { "evidence": [ { "id": "rs1386857992", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386857992" }, { "id": "rs1386857992", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386857992" } ], "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 (STS->NTS).", "chr_id": "3", "chr_pos": "180615060", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S896", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9UFE4-1.876.876", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9UFE4-1.884.884", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9UFE4-1.892.892", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UFE4-1.894.894", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9UFE4-1.900.900", "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": "Q9UFE4-1.930.930", "start_pos": 930, "end_pos": 930, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1427971338", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427971338", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1427971338", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427971338", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KFPASSSLVGSPSRPSSASS", "down_seq": "SSNVKSKKSSK", "snv": [ { "evidence": [ { "id": "rs1427971338", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427971338" }, { "id": "rs1427971338", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427971338" } ], "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 (SSS->NSS).", "chr_id": "3", "chr_pos": "180614958", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S930", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "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": "Q9UFE4-1.892.892", "start_pos": 892, "end_pos": 892, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKGSRQSSRSPSHTSLSARS", "down_seq": "RSTSTSTSQSSIKVLELKFP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "site_lbl": "Ser892" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9UFE4-1.876.876", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9UFE4-1.884.884", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UFE4-1.894.894", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9UFE4-1.896.896", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9UFE4-1.900.900", "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": "Q9UFE4-1.900.900", "start_pos": 900, "end_pos": 900, "uniprot_canonical_ac": "Q9UFE4-1", "length": 941, "uniprot_id": "CCD39_HUMAN", "protein_name": "Coiled-coil domain-containing protein 39", "refseq_ac": "NP_852091", "refseq_name": "coiled-coil domain-containing protein 39", "gene_name": "CCDC39", "gene_names_uniprotkb": "CCDC39", "gene_names_refseq": "CCDC39; CFAP59; CILD14; FAP59", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSPSHTSLSARSSRSTSTST", "down_seq": "QSSIKVLELKFPASSSLVGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UFE4", "url": "https://www.uniprot.org/uniprotkb/Q9UFE4" } ], "site_lbl": "Ser900" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "884", "end_pos": "884" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "930", "end_pos": "930" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "892", "end_pos": "892" }, { "start_pos": "900", "end_pos": "900" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9UFE4-1.884.884", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9UFE4-1.892.892", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9UFE4-1.894.894", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9UFE4-1.896.896", "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": "O15467-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "O15467-1", "length": 120, "uniprot_id": "CCL16_HUMAN", "protein_name": "C-C motif chemokine 16", "refseq_ac": "NP_004581", "refseq_name": "C-C motif chemokine 16 precursor", "gene_name": "CCL16", "gene_names_uniprotkb": "CCL16; ILINCK; NCC4; SCYA16", "gene_names_refseq": "CCL16; CKb12; HCC-4; ILINCK; LCC-1; LEC; LMC; Mtn-1; NCC-4; NCC4; SCYA16; SCYL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15467", "url": "https://www.uniprot.org/uniprotkb/O15467" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15467", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15467", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MKVSEAALSLLVLILIIT", "down_seq": "ASRSQPKVPEWVNTPSTCCL", "snv": [ { "evidence": [ { "id": "O15467", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15467" } ], "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 (3).", "chr_id": "17", "chr_pos": "35981365", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S19", "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: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": "snv", "site_list": [ { "start_pos": "19", "end_pos": "19" } ] } ], "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": "P62955-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ENILKTVRTATPFPMVSLFL", "down_seq": "FTAFVISNIGHIRPQRTILA", "snv": [ { "evidence": [ { "id": "P62955", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "53915412", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V111", "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: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": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P62955-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P62955-1.121.121", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P62955-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "TVRTATPFPMVSLFLVFTAF", "down_seq": "ISNIGHIRPQRTILAFVSGI", "snv": [ { "evidence": [ { "id": "P62955", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955" } ], "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": "19", "chr_pos": "53915427", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V116", "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: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": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P62955-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P62955-1.121.121", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P62955-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TPFPMVSLFLVFTAFVISNI", "down_seq": "HIRPQRTILAFVSGIFFILS", "snv": [ { "evidence": [ { "id": "P62955", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "53915442", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G121", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P62955-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P62955-1.116.116", "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": "P62955-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FILSGLSLVVGLVLYISSIN", "down_seq": "EVMNRPSSSEQYFHYRYGWS", "snv": [ { "evidence": [ { "id": "P62955", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955" } ], "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": "53941517", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D158", "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": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P62955-1.174.174", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P62955-1.174.174", "start_pos": 174, "end_pos": 174, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SSINDEVMNRPSSSEQYFHY", "down_seq": "YGWSFAFAASSFLLKEGAGV", "snv": [ { "evidence": [ { "id": "P62955", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "53941566", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R174", "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": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P62955-1.158.158", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P62955-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MSHCSSRALTLLSSVFG", "down_seq": "CGLLLVGIAVSTDYWLYMEE", "snv": [ { "evidence": [ { "id": "P62955", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955" } ], "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 (7).", "chr_id": "19", "chr_pos": "53912884", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A18", "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: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: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": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "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": "P62955-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KRYAEEEMYRPHPAFYRPRL", "down_seq": "DCSDYSGQFLQPEAWRRGRS", "snv": [ { "evidence": [ { "id": "P62955", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "19", "chr_pos": "53942130", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S222", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "site_lbl": "Ser222" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P62955-1.225.225", "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": 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": "P62955-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "REKGRCVASEYFLEPEINLV", "down_seq": "ENTENILKTVRTATPFPMVS", "snv": [ { "evidence": [ { "id": "P62955", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62955" } ], "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 (4).", "chr_id": "19", "chr_pos": "53914563", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T87", "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": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "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": "P62955-1.225.225", "start_pos": 225, "end_pos": 225, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AEEEMYRPHPAFYRPRLSDC", "down_seq": "DYSGQFLQPEAWRRGRSPSD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "site_lbl": "Ser225" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P62955-1.222.222", "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": 0 } ], "sort_fields": [] } ] }, { "id": "P62955-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "P62955-1", "length": 275, "uniprot_id": "CCG7_HUMAN", "protein_name": "Voltage-dependent calcium channel gamma-7 subunit", "refseq_ac": "NP_114102", "refseq_name": "voltage-dependent calcium channel gamma-7 subunit isoform 1", "gene_name": "CACNG7", "gene_names_uniprotkb": "CACNG7", "gene_names_refseq": "CACNG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QMTQNYPPAIKYPDHLHIST", "down_seq": "PC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P62955", "url": "https://www.uniprot.org/uniprotkb/P62955" } ], "site_lbl": "Ser273" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "273", "end_pos": "273" } ] } ], "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": "P15169-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "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": "rs371070915", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371070915", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371070915", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371070915", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371070915", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371070915#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371070915", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371070915", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PYDKSFEHRVRGVRRTASTP", "down_seq": "PDDKLFQKLAKVYSYAHGWM", "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": "Thr245", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs371070915", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371070915" }, { "id": "rs371070915", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371070915" }, { "id": "rs371070915", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371070915#frequency_tab" }, { "id": "rs371070915", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371070915" } ], "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": "10", "chr_pos": "100065213", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T245", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" }, { "id": "rs371070915", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371070915" }, { "id": "rs371070915", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371070915" }, { "id": "rs371070915", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371070915#frequency_tab" }, { "id": "rs371070915", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371070915" } ], "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: o-glyco-site-loss (T->M).", "chr_id": "10", "chr_pos": "100065213", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T245", "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", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P15169-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P15169-1.241.241", "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": "P15169-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of the human carboxypeptidase N (kininase I) catalytic domain.", "journal": "Journal of molecular biology", "date": "2007", "authors": "Keil C, Maskos K, Than M, Hoopes JT, Huber R, Tan F, Deddish PA, Erdos EG, Skidgel RA, Bode W", "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169#ptm_processing" }, { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "reference": [ { "type": "PubMed", "id": "17157876", "url": "https://glygen.org/publication/PubMed/17157876" } ] } ], "crossref": [ { "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17157876", "url": "https://glygen.org/publication/PubMed/17157876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2NSM", "url": "https://www.rcsb.org/structure/2NSM", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2NSM|A|380", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs780243866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780243866", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780243866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780243866", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780243866", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780243866#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780243866", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780243866", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLPGIYTVSATAPGYDPETV", "down_seq": "VTVGPAEPTLVNFHLKRSIP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=2NSM&bu=0&command=select+.A:380;+center+selection;+zoom+selection" }, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr400", "evidence": [ { "id": "P15169", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15169#ptm_processing" }, { "id": "17157876", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/17157876" }, { "id": "2NSM", "database": "PDB", "url": "https://www.rcsb.org/structure/2NSM" } ] } ], "snv": [ { "evidence": [ { "id": "rs780243866", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780243866" }, { "id": "rs780243866", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780243866" }, { "id": "rs780243866", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780243866#frequency_tab" }, { "id": "rs780243866", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780243866" } ], "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": "10", "chr_pos": "100048789", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T400", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P15169-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15169-1.409.409", "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": 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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P15169-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of the human carboxypeptidase N (kininase I) catalytic domain.", "journal": "Journal of molecular biology", "date": "2007", "authors": "Keil C, Maskos K, Than M, Hoopes JT, Huber R, Tan F, Deddish PA, Erdos EG, Skidgel RA, Bode W", "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169#ptm_processing" }, { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "reference": [ { "type": "PubMed", "id": "17157876", "url": "https://glygen.org/publication/PubMed/17157876" } ] } ], "crossref": [ { "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17157876", "url": "https://glygen.org/publication/PubMed/17157876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "2NSM", "url": "https://www.rcsb.org/structure/2NSM", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2NSM|A|382", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PGIYTVSATAPGYDPETVTV", "down_seq": "VGPAEPTLVNFHLKRSIPQV", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=2NSM&bu=0&command=select+.A:382;+center+selection;+zoom+selection" }, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr402", "evidence": [ { "id": "P15169", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15169#ptm_processing" }, { "id": "17157876", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/17157876" }, { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" }, { "id": "2NSM", "database": "PDB", "url": "https://www.rcsb.org/structure/2NSM" } ] } ], "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); o-glyco-site-loss (T->I).", "chr_id": "10", "chr_pos": "100048783", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T402", "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: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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P15169-1.400.400", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15169-1.409.409", "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": 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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "P15169-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of the human carboxypeptidase N (kininase I) catalytic domain.", "journal": "Journal of molecular biology", "date": "2007", "authors": "Keil C, Maskos K, Than M, Hoopes JT, Huber R, Tan F, Deddish PA, Erdos EG, Skidgel RA, Bode W", "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169#ptm_processing" }, { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "reference": [ { "type": "PubMed", "id": "17157876", "url": "https://glygen.org/publication/PubMed/17157876" } ] } ], "crossref": [ { "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17157876", "url": "https://glygen.org/publication/PubMed/17157876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2NSM", "url": "https://www.rcsb.org/structure/2NSM", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2NSM|A|389", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs143121841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143121841", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143121841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143121841", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143121841", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143121841#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143121841", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143121841", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ATAPGYDPETVTVTVGPAEP", "down_seq": "LVNFHLKRSIPQVSPVRRAP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=2NSM&bu=0&command=select+.A:389;+center+selection;+zoom+selection" }, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr409", "evidence": [ { "id": "P15169", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15169#ptm_processing" }, { "id": "17157876", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/17157876" }, { "id": "2NSM", "database": "PDB", "url": "https://www.rcsb.org/structure/2NSM" } ] } ], "snv": [ { "evidence": [ { "id": "rs143121841", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143121841" }, { "id": "rs143121841", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143121841" }, { "id": "rs143121841", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143121841#frequency_tab" }, { "id": "rs143121841", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143121841" } ], "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": "10", "chr_pos": "100048762", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T409", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs143121841", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143121841" }, { "id": "rs143121841", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143121841" }, { "id": "rs143121841", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143121841#frequency_tab" }, { "id": "rs143121841", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143121841" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "10", "chr_pos": "100048762", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T409", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->R).", "chr_id": "10", "chr_pos": "100048762", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T409", "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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P15169-1.400.400", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15169-1.402.402", "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": 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": 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": "P15169-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs940408104", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs940408104", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs940408104", "url": "https://www.ncbi.nlm.nih.gov/snp/rs940408104#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs940408104", "url": "http://gnomad.broadinstitute.org/awesome?query=rs940408104", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RELMLQLSEFLCEEFRNRNQ", "down_seq": "IVQLIQDTRIHILPSMNPDG", "snv": [ { "evidence": [ { "id": "rs940408104", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs940408104" }, { "id": "rs940408104", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs940408104#frequency_tab" }, { "id": "rs940408104", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs940408104" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQR->NQC).", "chr_id": "10", "chr_pos": "100075994", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R113", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs940408104", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs940408104" }, { "id": "rs940408104", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs940408104#frequency_tab" }, { "id": "rs940408104", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs940408104" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQR->NQS).", "chr_id": "10", "chr_pos": "100075994", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R113", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P15169-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15169-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15169-1.122.122", "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": 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": "P15169-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LMLQLSEFLCEEFRNRNQRI", "down_seq": "QLIQDTRIHILPSMNPDGYE", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "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": "10", "chr_pos": "100075988", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V115", "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: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: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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P15169-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15169-1.122.122", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FLCEEFRNRNQRIVQLIQDT", "down_seq": "IHILPSMNPDGYEVAAAQGP", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "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 (3).", "chr_id": "10", "chr_pos": "100075966", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R122", "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: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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P15169-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15169-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753130759", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753130759", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753130759", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753130759", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753130759", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753130759", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EVAAAQGPNKPGYLVGRNNA", "down_seq": "GVDLNRNFPDLNTYIYYNEK", "snv": [ { "evidence": [ { "id": "rs753130759", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753130759" }, { "id": "rs753130759", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753130759" }, { "id": "rs753130759", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753130759" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAN->NAS).", "chr_id": "10", "chr_pos": "100069826", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N155", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P15169-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15169-1.164.164", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs750449248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750449248", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750449248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750449248", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750449248", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750449248#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750449248", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750449248", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PNKPGYLVGRNNANGVDLNR", "down_seq": "FPDLNTYIYYNEKYGGPNHH", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" }, { "id": "rs750449248", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750449248" }, { "id": "rs750449248", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750449248" }, { "id": "rs750449248", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750449248#frequency_tab" }, { "id": "rs750449248", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750449248" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRN->NRS).", "chr_id": "10", "chr_pos": "100069805", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N162", "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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P15169-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15169-1.164.164", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs867591864", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867591864", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs867591864", "url": "https://www.ensembl.org/id/rs867591864", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KPGYLVGRNNANGVDLNRNF", "down_seq": "DLNTYIYYNEKYGGPNHHLP", "snv": [ { "evidence": [ { "id": "rs867591864", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867591864" }, { "id": "rs867591864", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs867591864" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFP->NFS).", "chr_id": "10", "chr_pos": "100069800", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P164", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NFP->NFT).", "chr_id": "10", "chr_pos": "100069800", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P164", "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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P15169-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15169-1.162.162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P15169-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PNHHLPLPDNWKSQVEPETR", "down_seq": "VIRWMHSFNFVLSANLHGGA", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "100065351", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A199", "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: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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "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": "P15169-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GAVVANYPYDKSFEHRVRGV", "down_seq": "RTASTPTPDDKLFQKLAKVY", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "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": "10", "chr_pos": "100065235", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R238", "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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P15169-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15169-1.245.245", "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": "P15169-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VANYPYDKSFEHRVRGVRRT", "down_seq": "STPTPDDKLFQKLAKVYSYA", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "100065226", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A241", "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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P15169-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P15169-1.245.245", "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": "P15169-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VFLHLLLLFKLVAPVTFRHH", "down_seq": "YDDLVRTLYKVQNECPGITR", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "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": "10", "chr_pos": "100081546", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R27", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P15169-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15169-1.41.41", "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": "P15169-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1455805925", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1455805925", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1455805925", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1455805925", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GWMFQGWNCGDYFPDGITNG", "down_seq": "SWYSLSKGMQDFNYLHTNCF", "snv": [ { "evidence": [ { "id": "rs1455805925", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1455805925" }, { "id": "rs1455805925", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1455805925" } ], "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": "10", "chr_pos": "100063638", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A283", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "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": "P15169-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "WLGNREALIQFLEQVHQGIK", "down_seq": "MVLDENYNNLANAVISVSGI", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "100054427", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G344", "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: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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P15169-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15169-1.355.355", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.352.352", "start_pos": 352, "end_pos": 352, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759543168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759543168", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759543168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759543168", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759543168", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759543168#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759543168", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759543168", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IQFLEQVHQGIKGMVLDENY", "down_seq": "NLANAVISVSGINHDVTSGD", "snv": [ { "evidence": [ { "id": "rs759543168", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759543168" }, { "id": "rs759543168", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759543168" }, { "id": "rs759543168", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759543168#frequency_tab" }, { "id": "rs759543168", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759543168" } ], "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": "10", "chr_pos": "100054403", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N352", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P15169-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15169-1.355.355", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771923245", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771923245", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771923245", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771923245", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771923245", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771923245#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771923245", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771923245", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LEQVHQGIKGMVLDENYNNL", "down_seq": "NAVISVSGINHDVTSGDHGD", "snv": [ { "evidence": [ { "id": "rs771923245", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771923245" }, { "id": "rs771923245", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771923245" }, { "id": "rs771923245", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771923245#frequency_tab" }, { "id": "rs771923245", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771923245" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLS).", "chr_id": "10", "chr_pos": "100054395", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A355", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771923245", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771923245" }, { "id": "rs771923245", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771923245" }, { "id": "rs771923245", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771923245#frequency_tab" }, { "id": "rs771923245", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771923245" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLT).", "chr_id": "10", "chr_pos": "100054395", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A355", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P15169-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15169-1.352.352", "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": 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": "P15169-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VTFRHHRYDDLVRTLYKVQN", "down_seq": "CPGITRVYSIGRSVEGRHLY", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "7", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "100081505", "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: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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P15169-1.27.27", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.89.89", "start_pos": 89, "end_pos": 89, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PGIHEPLEPEVKYVGNMHGN", "down_seq": "ALGRELMLQLSEFLCEEFRN", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "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": "10", "chr_pos": "100076066", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E89", "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: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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P15169-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P15169-1.93.93", "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": "P15169-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1188160239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1188160239", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1188160239", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1188160239", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GIHEPLEPEVKYVGNMHGNE", "down_seq": "LGRELMLQLSEFLCEEFRNR", "snv": [ { "evidence": [ { "id": "rs1188160239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1188160239" }, { "id": "rs1188160239", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1188160239" } ], "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": "10", "chr_pos": "100076063", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A90", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P15169-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15169-1.93.93", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EPLEPEVKYVGNMHGNEALG", "down_seq": "ELMLQLSEFLCEEFRNRNQR", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "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": "10", "chr_pos": "100076053", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R93", "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: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: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": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P15169-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15169-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P15169-1.113.113", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15169-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "P15169-1", "length": 458, "uniprot_id": "CBPN_HUMAN", "protein_name": "Carboxypeptidase N catalytic chain", "refseq_ac": "NP_001299", "refseq_name": "carboxypeptidase N catalytic chain precursor", "gene_name": "CPN1", "gene_names_uniprotkb": "CPN1; ACBP", "gene_names_refseq": "CPN1; CPN; SCPN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15169", "url": "https://www.uniprot.org/uniprotkb/P15169" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15169", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MSDLLSVF", "down_seq": "HLLLLFKLVAPVTFRHHRYD", "snv": [ { "evidence": [ { "id": "P15169", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15169" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "10", "chr_pos": "100081600", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L9", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P15169-1.27.27", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q68DN1-1.1066.1066", "start_pos": 1066, "end_pos": 1066, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "database": "O-GlcNAc Atlas", "id": "Q68DN1", "url": "https://oglcnac.org/atlas/detail/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "database": "O-GlcNAc Atlas", "id": "Q68DN1", "url": "https://oglcnac.org/atlas/detail/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68DN1", "url": "https://oglcnac.org/atlas/detail/Q68DN1", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MEESEDSQSDSQTRISESQH", "down_seq": "LKPNYLSQAKTDFSEQFQLL", "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": "Ser1066", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q68DN1", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q68DN1", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q68DN1" } ] } ], "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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": "2", "chr_pos": "27579769", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1066", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "Q68DN1-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "database": "O-GlcNAc Atlas", "id": "Q68DN1", "url": "https://oglcnac.org/atlas/detail/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "database": "O-GlcNAc Atlas", "id": "Q68DN1", "url": "https://oglcnac.org/atlas/detail/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68DN1", "url": "https://oglcnac.org/atlas/detail/Q68DN1", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TEAMGLTAEARIQANEFFGM", "down_seq": "PKPTSQATGFAERSPRLCPQ", "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": "Thr294", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q68DN1", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q68DN1", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q68DN1" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68DN1-1.361.361", "start_pos": 361, "end_pos": 361, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "database": "O-GlcNAc Atlas", "id": "Q68DN1", "url": "https://oglcnac.org/atlas/detail/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "database": "O-GlcNAc Atlas", "id": "Q68DN1", "url": "https://oglcnac.org/atlas/detail/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68DN1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HHVPDSASGMTPGLGHRVPE", "down_seq": "VELTSKSGVQVEKTLQLTPK", "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": "Ser361", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q68DN1", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DN1" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "2", "chr_pos": "27577653", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S361", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "Q68DN1-1.464.464", "start_pos": 464, "end_pos": 464, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1", "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": "REVSMGLTKSKNQSMKSPGT", "down_seq": "PGPLGRIVEFMRISPEPLDQ", "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": "Thr464", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Thr464" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q68DN1-1.463.463", "categories": [ "phosphorylation_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": 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": 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": "Q68DN1-1.516.516", "start_pos": 516, "end_pos": 516, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "AQSEEVILIDVPKVVQSVKV", "down_seq": "PGPPFQIVKSVTIPRPTPQM", "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": "Thr516", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q68DN1-1.528.528", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68DN1-1.533.533", "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": "Q68DN1-1.533.533", "start_pos": 533, "end_pos": 533, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "VKVTPGPPFQIVKSVTIPRP", "down_seq": "PQMVEYIELTPKLQYVRPSE", "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": "Thr533", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q68DN1-1.516.516", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q68DN1-1.528.528", "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": 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": "Q68DN1-1.1140.1140", "start_pos": 1140, "end_pos": 1140, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ICLQCGRCSGLNCHHKLQTT", "down_seq": "GPYLLIYPQLHLVRTPEGHG", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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: num. of cancers (3).", "chr_id": "2", "chr_pos": "27579991", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1140", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.1282.1282", "start_pos": 1282, "end_pos": 1282, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LPESDSESTQNEKRAKVRTK", "down_seq": "TSDSKYPMKRITKRLRKHRK", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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": "2", "chr_pos": "27580418", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K1282", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MELTPGAQQQGI", "down_seq": "YQELTSGWQDVKSMMLVPEP", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "27576609", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N13", "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: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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.1453.1453", "start_pos": 1453, "end_pos": 1453, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VQCRSAQQPRRAYSFQPRPL", "down_seq": "LPKPTDSQSGIAFQTASVGQ", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "2", "chr_pos": "27580929", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1453", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.1523.1523", "start_pos": 1523, "end_pos": 1523, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LSTPGTRVQARGRILPGSPV", "down_seq": "RTWHRHLKDKLTHKEHNHPS", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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 (KRT->NRT).", "chr_id": "2", "chr_pos": "27581141", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K1523", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.1567.1567", "start_pos": 1567, "end_pos": 1567, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ERTPRGPSERTRHNPSWRNH", "down_seq": "SPSERSQRSSLERRHHSPSQ", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NHR->NHC).", "chr_id": "2", "chr_pos": "27581271", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1567", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.1655.1655", "start_pos": 1655, "end_pos": 1655, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QRSHRGPSQRRHHSPSERSH", "down_seq": "SPSERSHRSSSERRHRSPSQ", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "27581536", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1655", "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: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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q68DN1-1.1663.1663", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DN1-1.1663.1663", "start_pos": 1663, "end_pos": 1663, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QRRHHSPSERSHRSPSERSH", "down_seq": "SSSERRHRSPSQRSHRGPSE", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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": "2", "chr_pos": "27581560", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1663", "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": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q68DN1-1.1655.1655", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DN1-1.1685.1685", "start_pos": 1685, "end_pos": 1685, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSERRHRSPSQRSHRGPSER", "down_seq": "HCSPSERRHRSPSQRSHRGP", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SHC->NHC).", "chr_id": "2", "chr_pos": "27581626", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1685", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.1732.1732", "start_pos": 1732, "end_pos": 1732, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SPSKRSHRSPARRSHRSPSE", "down_seq": "SHHSPSERSHHSPSERRHHS", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "27581767", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1732", "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: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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.1757.1757", "start_pos": 1757, "end_pos": 1757, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSERSHHSPSERRHHSPSER", "down_seq": "HCSPSERSHCSPSERRHRSP", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SHC->NHC).", "chr_id": "2", "chr_pos": "27581842", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1757", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q68DN1-1.1758.1758", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q68DN1-1.1773.1773", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q68DN1-1.1775.1775", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DN1-1.1758.1758", "start_pos": 1758, "end_pos": 1758, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SERSHHSPSERRHHSPSERS", "down_seq": "CSPSERSHCSPSERRHRSPS", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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 (HCS->NCS).", "chr_id": "2", "chr_pos": "27581844", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H1758", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q68DN1-1.1757.1757", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q68DN1-1.1773.1773", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68DN1-1.1775.1775", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DN1-1.1773.1773", "start_pos": 1773, "end_pos": 1773, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PSERSHCSPSERSHCSPSER", "down_seq": "HRSPSERRHHSPSEKSHHSP", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "27581891", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R1773", "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: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: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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q68DN1-1.1757.1757", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q68DN1-1.1758.1758", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q68DN1-1.1775.1775", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DN1-1.1775.1775", "start_pos": 1775, "end_pos": 1775, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ERSHCSPSERSHCSPSERRH", "down_seq": "SPSERRHHSPSEKSHHSPSE", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "27581895", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1775", "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: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: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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q68DN1-1.1757.1757", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q68DN1-1.1758.1758", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q68DN1-1.1773.1773", "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": "Q68DN1-1.267.267", "start_pos": 267, "end_pos": 267, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DVGELYMKPLQQTVEYEGIT", "down_seq": "ELKHYFTEAMGLTAEARIQA", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "27577372", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P267", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.528.528", "start_pos": 528, "end_pos": 528, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KVVQSVKVTPGPPFQIVKSV", "down_seq": "IPRPTPQMVEYIELTPKLQY", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "27578155", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T528", "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: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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q68DN1-1.516.516", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68DN1-1.533.533", "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": "Q68DN1-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "TSVRFSNLSPESQQQDVKSL", "down_seq": "FTVEPKLQSVKHVKLSSVSL", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "27576762", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E64", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.802.802", "start_pos": 802, "end_pos": 802, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IDPTMIQSLTFPLALHNQSS", "down_seq": "KTANIVENPCPEILGVDVIS", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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 (DKT->NKT).", "chr_id": "2", "chr_pos": "27578976", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D802", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q68DN1-1.811.811", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DN1-1.811.811", "start_pos": 811, "end_pos": 811, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TFPLALHNQSSDKTANIVEN", "down_seq": "CPEILGVDVISKETTKRKQM", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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 (NPC->NSC).", "chr_id": "2", "chr_pos": "27568791", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P811", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q68DN1-1.802.802", "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": "Q68DN1-1.920.920", "start_pos": 920, "end_pos": 920, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DN1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GTTMERKLCSQTSLAERATA", "down_seq": "TCQSIQNLFGIPAELMEPSQ", "snv": [ { "evidence": [ { "id": "Q68DN1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DN1" } ], "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 (DTC->NTC).", "chr_id": "2", "chr_pos": "27579330", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D920", "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": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "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": "Q68DN1-1.463.463", "start_pos": 463, "end_pos": 463, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1", "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": "HREVSMGLTKSKNQSMKSPG", "down_seq": "TPGPLGRIVEFMRISPEPLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Thr463" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q68DN1-1.464.464", "categories": [ "glycosylation_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": "Q68DN1-1.687.687", "start_pos": 687, "end_pos": 687, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1", "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": "TSPFEEHTILTHKQGLQAVK", "down_seq": "TVIKTEPPKVMETEDLNLGH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser687" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q68DN1-1.692.692", "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": "Q68DN1-1.692.692", "start_pos": 692, "end_pos": 692, "uniprot_canonical_ac": "Q68DN1-1", "length": 1984, "uniprot_id": "S31H1_HUMAN", "protein_name": "Spermatogenesis-associated protein 31H1", "refseq_ac": "NP_115642", "refseq_name": "spermatogenesis-associated protein 31H1", "gene_name": "SPATA31H1", "gene_names_uniprotkb": "SPATA31H1; C2orf16", "gene_names_refseq": "C2orf16; SPATA31H1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DN1", "url": "https://www.uniprot.org/uniprotkb/Q68DN1" } ], "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": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1", "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": "EHTILTHKQGLQAVKSTVIK", "down_seq": "EPPKVMETEDLNLGHVCQNR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68DN1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DN1" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Thr692" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "533", "end_pos": "533" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "1453", "end_pos": "1453" }, { "start_pos": "1523", "end_pos": "1523" }, { "start_pos": "1567", "end_pos": "1567" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1758", "end_pos": "1758" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1775", "end_pos": "1775" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "920", "end_pos": "920" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "463", "end_pos": "463" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "692", "end_pos": "692" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q68DN1-1.687.687", "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": "H3BNL1-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "H3BNL1-1", "length": 204, "uniprot_id": "CMIP7_HUMAN", "protein_name": "Ciliary microtubule inner protein 7", "refseq_ac": "NP_001073997", "refseq_name": "ciliary microtubule inner protein 7", "gene_name": "CIMIP7", "gene_names_uniprotkb": "CIMIP7; C3orf84", "gene_names_refseq": "C3orf84; CIMIP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "H3BNL1", "url": "https://www.uniprot.org/uniprotkb/H3BNL1" } ], "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": "rs775553571", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775553571", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775553571", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775553571", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775553571", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775553571", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2107662084", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2107662084", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2107662084", "url": "https://www.ensembl.org/id/rs2107662084", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GIPRPKLLQHYLHAGVSECL", "down_seq": "WSRALNKDS", "glycosylation": [ { "glytoucan_ac": "G68040BX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VGPQAPVTDVLPDLPGIPRPKLLQHYLHAGVSECLNWSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn195", "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": "rs775553571", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775553571" }, { "id": "rs775553571", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775553571" }, { "id": "rs775553571", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775553571" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NWS->TWS).", "chr_id": "3", "chr_pos": "49177667", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N195", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2107662084", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2107662084" }, { "id": "rs2107662084", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2107662084" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NWS->YWS).", "chr_id": "3", "chr_pos": "49177668", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N195", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "195", "end_pos": "195" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "H3BNL1-1.197.197", "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": "H3BNL1-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "H3BNL1-1", "length": 204, "uniprot_id": "CMIP7_HUMAN", "protein_name": "Ciliary microtubule inner protein 7", "refseq_ac": "NP_001073997", "refseq_name": "ciliary microtubule inner protein 7", "gene_name": "CIMIP7", "gene_names_uniprotkb": "CIMIP7; C3orf84", "gene_names_refseq": "C3orf84; CIMIP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "H3BNL1", "url": "https://www.uniprot.org/uniprotkb/H3BNL1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "H3BNL1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/H3BNL1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MQSALVGSWHNNG", "down_seq": "YGHYRSQFKSESAREYHLAA", "snv": [ { "evidence": [ { "id": "H3BNL1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/H3BNL1" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGF->NGC).", "chr_id": "3", "chr_pos": "49190125", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F14", "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": "195", "end_pos": "195" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" } ] } ], "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": "H3BNL1-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "H3BNL1-1", "length": 204, "uniprot_id": "CMIP7_HUMAN", "protein_name": "Ciliary microtubule inner protein 7", "refseq_ac": "NP_001073997", "refseq_name": "ciliary microtubule inner protein 7", "gene_name": "CIMIP7", "gene_names_uniprotkb": "CIMIP7; C3orf84", "gene_names_refseq": "C3orf84; CIMIP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "H3BNL1", "url": "https://www.uniprot.org/uniprotkb/H3BNL1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2045842831", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2045842831", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2045842831", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2045842831#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PRPKLLQHYLHAGVSECLNW", "down_seq": "RALNKDS", "snv": [ { "evidence": [ { "id": "rs2045842831", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2045842831" }, { "id": "rs2045842831", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2045842831#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 (NWS->NWF).", "chr_id": "3", "chr_pos": "49177661", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S197", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "195", "end_pos": "195" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "H3BNL1-1.195.195", "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": "H7C350-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "H7C350-1", "length": 402, "uniprot_id": "CC188_HUMAN", "protein_name": "Coiled-coil domain-containing protein 188", "refseq_ac": "NP_001352821", "refseq_name": "coiled-coil domain-containing protein 188", "gene_name": "CCDC188", "gene_names_uniprotkb": "CCDC188", "gene_names_refseq": "CCDC188", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "H7C350", "url": "https://www.uniprot.org/uniprotkb/H7C350" } ], "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": "", "down_seq": "PASSSHGGGLDQPCQGFVGW", "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": "Thr20", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "snv", "site_list": [ { "start_pos": "69", "end_pos": "69" } ] } ], "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": "H7C350-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "H7C350-1", "length": 402, "uniprot_id": "CC188_HUMAN", "protein_name": "Coiled-coil domain-containing protein 188", "refseq_ac": "NP_001352821", "refseq_name": "coiled-coil domain-containing protein 188", "gene_name": "CCDC188", "gene_names_uniprotkb": "CCDC188", "gene_names_refseq": "CCDC188", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "H7C350", "url": "https://www.uniprot.org/uniprotkb/H7C350" } ], "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": "rs2050613034", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2050613034", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2050613034", "url": "https://www.ensembl.org/id/rs2050613034", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AHSVQSQRPFPVPGAGGSGP", "down_seq": "VEGEAPGLFLSSQEQRARDT", "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": "Thr69", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs2050613034", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2050613034" }, { "id": "rs2050613034", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2050613034" } ], "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": "22", "chr_pos": "20150781", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T69", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "snv", "site_list": [ { "start_pos": "69", "end_pos": "69" } ] } ], "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": "P32248-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1161074222", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1161074222", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1161074222", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1161074222#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1161074222", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1161074222", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LVIFQVCLCQDEVTDDYIGD", "down_seq": "TTVDYTLFESLCSKKDVRNF", "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": "Asn36", "evidence": [ { "id": "P32248", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P32248#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1161074222", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1161074222" }, { "id": "rs1161074222", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1161074222#frequency_tab" }, { "id": "rs1161074222", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1161074222" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->STT).", "chr_id": "17", "chr_pos": "40555772", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N36", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P32248-1.40.40", "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": "P32248-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P32248", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs775899752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775899752", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775899752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775899752", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775899752", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775899752#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775899752", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775899752", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs775899752", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs775899752", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TVANFNITSSTCELSKQLNI", "down_seq": "YDVTYSLACVRCCVNPFLYA", "snv": [ { "evidence": [ { "id": "P32248", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248" }, { "id": "rs775899752", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775899752" }, { "id": "rs775899752", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775899752" }, { "id": "rs775899752", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775899752#frequency_tab" }, { "id": "rs775899752", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775899752" }, { "id": "rs775899752", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs775899752" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-gain (NIA->NIT).", "chr_id": "17", "chr_pos": "40554960", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A307", "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", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P32248-1.309.309", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P32248-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P32248", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WVFGVHFCKLIFAIYKMSFF", "down_seq": "GMLLLLCISIDRYVAIVQAV", "snv": [ { "evidence": [ { "id": "P32248", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "40555455", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S142", "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": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P32248-1.155.155", "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": "P32248-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2036571914", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2036571914", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2036571914", "url": "https://www.ensembl.org/id/rs2036571914", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VAIVQAVSAHRHRARVLLIS", "down_seq": "LSCVGIWILATVLSIPELLY", "snv": [ { "evidence": [ { "id": "rs2036571914", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2036571914" }, { "id": "rs2036571914", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2036571914" } ], "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": "17", "chr_pos": "40555351", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K176", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "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": "P32248-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P32248", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LSIPELLYSDLQRSSSEQAM", "down_seq": "CSLITEHVEAFITIQVAQMV", "snv": [ { "evidence": [ { "id": "P32248", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "40555254", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R209", "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: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": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "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": "P32248-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P32248", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MVIGFLVPLLAMSFCYLVII", "down_seq": "TLLQARNFERNKAIKVIIAV", "snv": [ { "evidence": [ { "id": "P32248", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248" } ], "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": "40555137", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R248", "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": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P32248-1.261.261", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P32248-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764245161", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764245161", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764245161", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764245161#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764245161", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764245161", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764245161", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764245161", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1399630591", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399630591", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1399630591", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399630591", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FCYLVIIRTLLQARNFERNK", "down_seq": "IKVIIAVVVVFIVFQLPYNG", "snv": [ { "evidence": [ { "id": "rs764245161", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764245161" }, { "id": "rs764245161", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764245161#frequency_tab" }, { "id": "rs764245161", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764245161" }, { "id": "rs764245161", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764245161" }, { "id": "rs1399630591", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399630591" }, { "id": "rs1399630591", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399630591" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKA->NKS).", "chr_id": "17", "chr_pos": "40555080", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A261", "keywords": [ "ebi", "somatic", "germline" ] }, { "evidence": [ { "id": "rs764245161", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764245161" }, { "id": "rs764245161", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764245161#frequency_tab" }, { "id": "rs764245161", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764245161" }, { "id": "rs764245161", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764245161" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKA->NKT).", "chr_id": "17", "chr_pos": "40555080", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A261", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P32248-1.248.248", "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": 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": "P32248-1.309.309", "start_pos": 309, "end_pos": 309, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771282973", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771282973", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771282973", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771282973", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771282973", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771282973#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771282973", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771282973", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ANFNITSSTCELSKQLNIAY", "down_seq": "VTYSLACVRCCVNPFLYAFI", "snv": [ { "evidence": [ { "id": "rs771282973", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771282973" }, { "id": "rs771282973", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771282973" }, { "id": "rs771282973", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771282973#frequency_tab" }, { "id": "rs771282973", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771282973" } ], "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": "17", "chr_pos": "40554954", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D309", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P32248-1.307.307", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P32248-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P32248", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QVCLCQDEVTDDYIGDNTTV", "down_seq": "YTLFESLCSKKDVRNFKAWF", "snv": [ { "evidence": [ { "id": "P32248", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P32248" } ], "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 (DYT->NYT).", "chr_id": "17", "chr_pos": "40555761", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D40", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P32248-1.36.36", "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": "P32248-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P32248-1", "length": 378, "uniprot_id": "CCR7_HUMAN", "protein_name": "C-C chemokine receptor type 7", "refseq_ac": "NP_001288643", "refseq_name": "C-C chemokine receptor type 7 isoform b", "gene_name": "CCR7", "gene_names_uniprotkb": "CCR7; CMKBR7; EBI1; EVI1", "gene_names_refseq": "BLR2; CC-CKR-7; CCR-7; CCR7; CD197; CDw197; CMKBR7; EBI1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P32248", "url": "https://www.uniprot.org/uniprotkb/P32248" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "CCR7 Is Recruited to the Immunological Synapse, Acts as Co-stimulatory Molecule and Drives LFA-1 Clustering for Efficient T Cell Adhesion Through ZAP70.", "journal": "Frontiers in immunology", "date": "2018", "authors": "Laufer JM, Kindinger I, Artinger M, Pauli A, Legler DF", "evidence": [ { "database": "iPTMnet", "id": "P32248", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P32248" } ], "reference": [ { "type": "PubMed", "id": "30692994", "url": "https://glygen.org/publication/PubMed/30692994" } ] } ], "crossref": [ { "id": "P32248", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P32248", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "30692994", "url": "https://glygen.org/publication/PubMed/30692994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IYKMSFFSGMLLLLCISIDR", "down_seq": "VAIVQAVSAHRHRARVLLIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P32248", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P32248" }, { "database": "PubMed", "id": "30692994", "url": "https://glygen.org/publication/PubMed/30692994" } ], "site_lbl": "Tyr155" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "snv", "site_list": [ { "start_pos": "307", "end_pos": "307" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P32248-1.142.142", "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": "O15234-1.443.443", "start_pos": 443, "end_pos": 443, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "rs752773013", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752773013", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752773013", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752773013", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752773013", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752773013#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752773013", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752773013", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EVPPPPEGLIPAPPVPETTP", "down_seq": "PPTKTGTWEAPVDSSTSGLE", "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": "Thr443", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs752773013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752773013" }, { "id": "rs752773013", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752773013" }, { "id": "rs752773013", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752773013#frequency_tab" }, { "id": "rs752773013", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752773013" } ], "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": "17", "chr_pos": "40164022", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T443", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "O15234-1.458.458", "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": "O15234-1.699.699", "start_pos": 699, "end_pos": 699, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O15234" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "O15234", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O15234" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "O15234", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O15234" }, { "database": "O-GlcNAc Atlas", "id": "O15234", "url": "https://oglcnac.org/atlas/detail/O15234" } ], "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": "O15234", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O15234" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O15234", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O15234" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "O15234", "url": "https://oglcnac.org/atlas/detail/O15234" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O15234", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "https://oglcnac.org/atlas/detail/O15234", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPPRRTPQPVTIKPPPPEVV", "down_seq": "RGSS", "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": "Ser699", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "O15234", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O15234" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" }, { "id": "O15234", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O15234" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O15234-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity.", "journal": "Nature structural & molecular biology", "date": "2005", "authors": "Ballut L, Marchadier B, Baguet A, Tomasetto C, Seraphin B, Le Hir H", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "reference": [ { "type": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KVGKKGPKHLDDDEDRKNPA", "down_seq": "IPRKGLFFEHDLRGQTQEEE", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Does not affect EJC formation.", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "O15234-1.184.185", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O15234-1.188.188", "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": "O15234-1.184.185", "start_pos": 184, "end_pos": 185, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity.", "journal": "Nature structural & molecular biology", "date": "2005", "authors": "Ballut L, Marchadier B, Baguet A, Tomasetto C, Seraphin B, Le Hir H", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "reference": [ { "type": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "RK", "start_aa": "R", "up_seq": "KKGPKHLDDDEDRKNPAYIP", "down_seq": "GLFFEHDLRGQTQEEEVRPK", "mutagenesis": [ { "sequence_org": "RK", "sequence_mut": "AA", "comment": "Does not affect EJC formation.", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O15234-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O15234-1.188.188", "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": "O15234-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity.", "journal": "Nature structural & molecular biology", "date": "2005", "authors": "Ballut L, Marchadier B, Baguet A, Tomasetto C, Seraphin B, Le Hir H", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "reference": [ { "type": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "KHLDDDEDRKNPAYIPRKGL", "down_seq": "FEHDLRGQTQEEEVRPKGRQ", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "Does not affect EJC formation.", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O15234-1.181.181", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O15234-1.184.185", "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": "O15234-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity.", "journal": "Nature structural & molecular biology", "date": "2005", "authors": "Ballut L, Marchadier B, Baguet A, Tomasetto C, Seraphin B, Le Hir H", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "reference": [ { "type": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "QEEEVRPKGRQRKLWKDEGR", "down_seq": "EHDKFREDEQAPKSRQELIA", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "A", "comment": "Abolishes interaction with EIF4A3, EJC formation and localization in nucleus speckles.", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O15234-1.220.221", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O15234-1.232.232", "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": "O15234-1.220.221", "start_pos": 220, "end_pos": 221, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity.", "journal": "Nature structural & molecular biology", "date": "2005", "authors": "Ballut L, Marchadier B, Baguet A, Tomasetto C, Seraphin B, Le Hir H", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "reference": [ { "type": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "HD", "start_aa": "H", "up_seq": "EEVRPKGRQRKLWKDEGRWE", "down_seq": "KFREDEQAPKSRQELIALYG", "mutagenesis": [ { "sequence_org": "HD", "sequence_mut": "AA", "comment": "Abolishes interaction with EIF4A3, EJC formation and localization in nucleus speckles.", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O15234-1.218.218", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O15234-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O15234-1.240.241", "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": "O15234-1.240.241", "start_pos": 240, "end_pos": 241, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity.", "journal": "Nature structural & molecular biology", "date": "2005", "authors": "Ballut L, Marchadier B, Baguet A, Tomasetto C, Seraphin B, Le Hir H", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "reference": [ { "type": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "YG", "start_aa": "Y", "up_seq": "HDKFREDEQAPKSRQELIAL", "down_seq": "YDIRSAHNPDDIKPRRIRKP", "mutagenesis": [ { "sequence_org": "YG", "sequence_mut": "AA", "comment": "Abolishes interaction with EIF4A3, EJC formation and localization in nucleus speckles.", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "16170325", "url": "https://glygen.org/publication/PubMed/16170325" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O15234-1.220.221", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "O15234-1.232.232", "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": "O15234-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MADRRRQRA", "down_seq": "QDTEDEESGASGSDSGGSPL", "snv": [ { "evidence": [ { "id": "O15234", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "40140577", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S10", "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" } ] }, { "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": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "O15234-1.28.28", "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": "O15234-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WKDEGRWEHDKFREDEQAPK", "down_seq": "RQELIALYGYDIRSAHNPDD", "snv": [ { "evidence": [ { "id": "O15234", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "40162811", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S232", "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": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O15234-1.218.218", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "O15234-1.220.221", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O15234-1.240.241", "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": "O15234-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1472271183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1472271183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1472271183", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1472271183#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1472271183", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1472271183", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HRHQGLGGTLPPRTFINRNA", "down_seq": "GTGRMSAPRNYSRSGGFKEG", "snv": [ { "evidence": [ { "id": "rs1472271183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1472271183" }, { "id": "rs1472271183", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1472271183#frequency_tab" }, { "id": "rs1472271183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1472271183" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAA->NAS).", "chr_id": "17", "chr_pos": "40163599", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A302", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "O15234-1.315.315", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O15234-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TFINRNAAGTGRMSAPRNYS", "down_seq": "SGGFKEGRAGFRPVEAGGQH", "snv": [ { "evidence": [ { "id": "O15234", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "40163639", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R315", "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: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": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O15234-1.302.302", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O15234-1.338.338", "start_pos": 338, "end_pos": 338, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GFKEGRAGFRPVEAGGQHGG", "down_seq": "SGETVKHEISYRSRRLEQTS", "snv": [ { "evidence": [ { "id": "O15234", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234" } ], "glycoeffect": [], "subjects_tested": "606", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "40163708", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R338", "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: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: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": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "O15234-1.357.357", "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": "O15234-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "rs1172693483", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172693483", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1172693483", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1172693483", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "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": "ESGASGSDSGGSPLRGGGSC", "down_seq": "GSAGGGGSGSLPSQRGGRTG", "snv": [ { "evidence": [ { "id": "rs1172693483", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172693483" }, { "id": "rs1172693483", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1172693483" } ], "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 (SGS->NGS).", "chr_id": "17", "chr_pos": "40140658", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S37", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser37" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O15234-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O15234-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O15234-1.45.45", "categories": [ "snv_flag", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "O15234-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1989380586", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1989380586", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1989380586", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1989380586#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1989380586", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1989380586", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PETTPTPPTKTGTWEAPVDS", "down_seq": "TSGLEQDVAQLNIAEQNWSP", "snv": [ { "evidence": [ { "id": "rs1989380586", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1989380586" }, { "id": "rs1989380586", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1989380586#frequency_tab" }, { "id": "rs1989380586", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1989380586" } ], "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 (STS->NTS).", "chr_id": "17", "chr_pos": "40164068", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S458", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O15234-1.443.443", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O15234-1.477.477", "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": "O15234-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "rs751804046", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751804046", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751804046", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751804046", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751804046", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751804046", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGGSPLRGGGSCSGSAGGGG", "down_seq": "GSLPSQRGGRTGALHLRRVE", "snv": [ { "evidence": [ { "id": "rs751804046", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751804046" }, { "id": "rs751804046", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751804046" }, { "id": "rs751804046", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751804046" } ], "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 (SGS->NGS).", "chr_id": "17", "chr_pos": "40140682", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S45", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Ser45" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O15234-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O15234-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "O15234-1.37.37", "categories": [ "snv_flag", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "O15234-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1413804562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1413804562", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1413804562", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1413804562#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1413804562", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1413804562", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "LRGMPNHIHMGAGPPPQFNR", "down_seq": "EEMGVQGGRAKRYSSQRQRP", "snv": [ { "evidence": [ { "id": "rs1413804562", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1413804562" }, { "id": "rs1413804562", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1413804562#frequency_tab" }, { "id": "rs1413804562", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1413804562" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRM->NRT).", "chr_id": "17", "chr_pos": "40166851", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M509", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "O15234-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O15234-1.523.523", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O15234-1.518.518", "start_pos": 518, "end_pos": 518, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MGAGPPPQFNRMEEMGVQGG", "down_seq": "AKRYSSQRQRPVPEPPAPPV", "snv": [ { "evidence": [ { "id": "O15234", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "40167513", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R518", "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: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": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O15234-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O15234-1.523.523", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O15234-1.535.535", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O15234-1.523.523", "start_pos": 523, "end_pos": 523, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPQFNRMEEMGVQGGRAKRY", "down_seq": "SQRQRPVPEPPAPPVHISIM", "snv": [ { "evidence": [ { "id": "O15234", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234" } ], "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 (3).", "chr_id": "17", "chr_pos": "40167529", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S523", "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": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O15234-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O15234-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O15234-1.535.535", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O15234-1.535.535", "start_pos": 535, "end_pos": 535, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QGGRAKRYSSQRQRPVPEPP", "down_seq": "PPVHISIMEGHYYDPLQFQG", "snv": [ { "evidence": [ { "id": "O15234", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "3", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "40167564", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A535", "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": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O15234-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O15234-1.523.523", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O15234-1.621.621", "start_pos": 621, "end_pos": 621, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1989504756", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1989504756", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1989504756", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1989504756#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PPPVSMSPGQPPPQQLLAPT", "down_seq": "FSAPGVMNFGNPSYPYAPGA", "snv": [ { "evidence": [ { "id": "rs1989504756", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1989504756" }, { "id": "rs1989504756", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1989504756#frequency_tab" } ], "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 (YFS->NFS).", "chr_id": "17", "chr_pos": "40168313", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y621", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": "O15234-1.670.670", "start_pos": 670, "end_pos": 670, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LYPNTQAPSQVYGGVTYYNP", "down_seq": "QQQVQPKPSPPRRTPQPVTI", "snv": [ { "evidence": [ { "id": "O15234", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O15234" } ], "glycoeffect": [], "subjects_tested": "3601", "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": "40169366", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A670", "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": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": "O15234-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DSEGEEGEYSEEENSKVELK", "down_seq": "EANDAVNSSTKEEKGEEKPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "site_lbl": "Ser117" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "O15234-1.125.125", "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": "O15234-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YSEEENSKVELKSEANDAVN", "down_seq": "STKEEKGEEKPDTKSTVTGE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser125" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O15234-1.117.117", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O15234-1.141.141", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O15234-1.143.143", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O15234-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DAVNSSTKEEKGEEKPDTKS", "down_seq": "VTGERQSGDGQESTEPVENK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Thr141" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O15234-1.125.125", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O15234-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O15234-1.148.148", "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": "O15234-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "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": "VNSSTKEEKGEEKPDTKSTV", "down_seq": "GERQSGDGQESTEPVENKVG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Thr143" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O15234-1.125.125", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O15234-1.141.141", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O15234-1.148.148", "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": "O15234-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] }, { "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "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": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KEEKGEEKPDTKSTVTGERQ", "down_seq": "GDGQESTEPVENKVGKKGPK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "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": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Ser148" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O15234-1.141.141", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O15234-1.143.143", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O15234-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DIRSAHNPDDIKPRRIRKPR", "down_seq": "GSPPQRDPNWNGERLNKSHR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr263" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O15234-1.265.265", "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": "O15234-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSAHNPDDIKPRRIRKPRYG", "down_seq": "PPQRDPNWNGERLNKSHRHQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser265" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O15234-1.263.263", "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": "O15234-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "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": "RASQDTEDEESGASGSDSGG", "down_seq": "PLRGGGSCSGSAGGGGSGSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser28" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O15234-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O15234-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O15234-1.37.37", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O15234-1.45.45", "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": "O15234-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GRSGETVKHEISYRSRRLEQ", "down_seq": "SVRDPSPEADAPVLGSPEKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "site_lbl": "Thr357" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O15234-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O15234-1.363.363", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O15234-1.373.373", "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": "O15234-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DEESGASGSDSGGSPLRGGG", "down_seq": "CSGSAGGGGSGSLPSQRGGR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "site_lbl": "Ser35" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O15234-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O15234-1.37.37", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O15234-1.45.45", "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": 0 } ], "sort_fields": [] } ] }, { "id": "O15234-1.363.363", "start_pos": 363, "end_pos": 363, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "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": "VKHEISYRSRRLEQTSVRDP", "down_seq": "PEADAPVLGSPEKEEAASEP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser363" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O15234-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O15234-1.373.373", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O15234-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RLEQTSVRDPSPEADAPVLG", "down_seq": "PEKEEAASEPPAAAPDAAPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser373" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O15234-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O15234-1.363.363", "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": "O15234-1.477.477", "start_pos": 477, "end_pos": 477, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSTSGLEQDVAQLNIAEQNW", "down_seq": "PGQPSFLQPRELRGMPNHIH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "site_lbl": "Ser477" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O15234-1.458.458", "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": "O15234-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "O15234-1", "length": 703, "uniprot_id": "CASC3_HUMAN", "protein_name": "Protein CASC3", "refseq_ac": "NP_031385", "refseq_name": "protein CASC3", "gene_name": "CASC3", "gene_names_uniprotkb": "CASC3; MLN51", "gene_names_refseq": "BTZ; CASC3; MLN51", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O15234", "url": "https://www.uniprot.org/uniprotkb/O15234" } ], "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": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234", "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": "GSLPSQRGGRTGALHLRRVE", "down_seq": "GGAKSAEESECESEDGIEGD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O15234", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O15234" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser66" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "699", "end_pos": "699" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "220", "end_pos": "221" }, { "start_pos": "240", "end_pos": "241" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "670", "end_pos": "670" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": "O00626-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O00626-1", "length": 93, "uniprot_id": "CCL22_HUMAN", "protein_name": "C-C motif chemokine 22", "refseq_ac": "NP_002981", "refseq_name": "C-C motif chemokine 22 precursor", "gene_name": "CCL22", "gene_names_uniprotkb": "CCL22; A-152E5.1; MDC; SCYA22", "gene_names_refseq": "A-152E5.1; ABCD-1; CCL22; DC/B-CK; MDC; SCYA22; STCP-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O00626", "url": "https://www.uniprot.org/uniprotkb/O00626" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "O00626", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O00626" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O00626", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O00626", "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": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "O00626", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O00626" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "29", "end_pos": "29" }, { "start_pos": "42", "end_pos": "42" } ] } ], "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": "O00626-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "O00626-1", "length": 93, "uniprot_id": "CCL22_HUMAN", "protein_name": "C-C motif chemokine 22", "refseq_ac": "NP_002981", "refseq_name": "C-C motif chemokine 22 precursor", "gene_name": "CCL22", "gene_names_uniprotkb": "CCL22; A-152E5.1; MDC; SCYA22", "gene_names_refseq": "A-152E5.1; ABCD-1; CCL22; DC/B-CK; MDC; SCYA22; STCP-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O00626", "url": "https://www.uniprot.org/uniprotkb/O00626" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O00626", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O00626", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LVVLVLLAVALQATEAGPYG", "down_seq": "NMEDSVCCRDYVRYRLPLRV", "snv": [ { "evidence": [ { "id": "O00626", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O00626" } ], "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": "16", "chr_pos": "57360448", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A29", "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: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": "29", "end_pos": "29" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "O00626-1.42.42", "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": "O00626-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "O00626-1", "length": 93, "uniprot_id": "CCL22_HUMAN", "protein_name": "C-C motif chemokine 22", "refseq_ac": "NP_002981", "refseq_name": "C-C motif chemokine 22 precursor", "gene_name": "CCL22", "gene_names_uniprotkb": "CCL22; A-152E5.1; MDC; SCYA22", "gene_names_refseq": "A-152E5.1; ABCD-1; CCL22; DC/B-CK; MDC; SCYA22; STCP-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O00626", "url": "https://www.uniprot.org/uniprotkb/O00626" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O00626", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O00626", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TEAGPYGANMEDSVCCRDYV", "down_seq": "YRLPLRVVKHFYWTSDSCPR", "snv": [ { "evidence": [ { "id": "O00626", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O00626" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "57360488", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R42", "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: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": "29", "end_pos": "29" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O00626-1.29.29", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76039-2.479.479", "start_pos": 479, "end_pos": 479, "uniprot_canonical_ac": "O76039-2", "length": 960, "uniprot_id": "CDKL5_HUMAN", "protein_name": "Cyclin-dependent kinase-like 5", "refseq_ac": "NP_001032420", "refseq_name": "cyclin-dependent kinase-like 5 isoform 1", "gene_name": "CDKL5", "gene_names_uniprotkb": "CDKL5; STK9", "gene_names_refseq": "CDKL5; CFAP247; DEE2; EIEE2; ISSX; STK9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" } ], "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": "O76039", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76039" }, { "database": "O-GlcNAc Atlas", "id": "O76039", "url": "https://oglcnac.org/atlas/detail/O76039" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" }, { "database": "iPTMnet", "id": "O76039", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O76039" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O76039", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76039", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "O76039", "url": "https://oglcnac.org/atlas/detail/O76039", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O76039", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76039", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1602286391", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1602286391", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O76039", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O76039", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QPNEKQSRHSYIDTIPQSSR", "down_seq": "PSYRTKAKSHGALSDSKSVS", "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": "Ser479", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "O76039", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76039" }, { "id": "O76039", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O76039" } ] } ], "snv": [ { "evidence": [ { "id": "O76039", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76039" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->R).", "chr_id": "23", "chr_pos": "18604361", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S479", "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" ] }, { "evidence": [ { "id": "rs1602286391", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1602286391" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->X).", "chr_id": "X", "chr_pos": "18604355_18604359", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S479", "disease": [ { "disease_id": "DOID:0080467", "recommended_name": { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "developmental and epileptic encephalopathy 2", "description": "A developmental and epileptic encephalopathy characterized by X-linked dominant inheritance of seizure onset in the first months of life, intellectual disability, and poor motor control that has_material_basis_in mutation in the CDKL5 gene on chromosome Xp22." }, "synonyms": [ { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "X-linked infantile spasm syndrome 2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "DEE2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "EIEE2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "early infantile epileptic encephalopathy 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy, 2", "description": "Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the CDKL5 gene." }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "CDKL5 early infantile epileptic encephalopathy", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "DEE2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "EIEE2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy, 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "early infantile epileptic encephalopathy caused by mutation in CDKL5", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "epileptic encephalopathy, early infantile, 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "epileptic encephalopathy, early infantile, type 2", "description": "" }, { "id": "MIM:300672", "resource": "MIM", "url": "https://www.omim.org/entry/300672", "name": "Developmental and epileptic encephalopathy 2", "description": "Developmental and epileptic encephalopathy 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "300672", "database": "MIM", "url": "https://www.omim.org/entry/300672" }, { "id": "0080467", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080467" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O76039", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O76039" } ], "site_lbl": "Ser479" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "479", "end_pos": "479" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "693", "end_pos": "693" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "788", "end_pos": "788" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "847", "end_pos": "847" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "919", "end_pos": "919" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "O76039-2.493.493", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "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": 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": "O76039-2.531.531", "start_pos": 531, "end_pos": 531, "uniprot_canonical_ac": "O76039-2", "length": 960, "uniprot_id": "CDKL5_HUMAN", "protein_name": "Cyclin-dependent kinase-like 5", "refseq_ac": "NP_001032420", "refseq_name": "cyclin-dependent kinase-like 5 isoform 1", "gene_name": "CDKL5", "gene_names_uniprotkb": "CDKL5; STK9", "gene_names_refseq": "CDKL5; CFAP247; DEE2; EIEE2; ISSX; STK9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" } ], "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": "rs778464010", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778464010", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778464010", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778464010", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778464010", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778464010", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1241623214", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1241623214", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1241623214", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1241623214#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1241623214", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1241623214", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSTSRYFPSSCLDLNSPTSP", "down_seq": "PTRHSDTRTLLSPSGRNNRN", "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": "Thr531", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs778464010", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778464010" }, { "id": "rs778464010", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778464010" }, { "id": "rs778464010", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778464010" } ], "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": "18604515", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T531", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1241623214", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1241623214" }, { "id": "rs1241623214", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1241623214#frequency_tab" }, { "id": "rs1241623214", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1241623214" } ], "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": "X", "chr_pos": "18604516", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T531", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080467", "recommended_name": { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "developmental and epileptic encephalopathy 2", "description": "A developmental and epileptic encephalopathy characterized by X-linked dominant inheritance of seizure onset in the first months of life, intellectual disability, and poor motor control that has_material_basis_in mutation in the CDKL5 gene on chromosome Xp22." }, "synonyms": [ { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "X-linked infantile spasm syndrome 2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "DEE2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "EIEE2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "early infantile epileptic encephalopathy 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy, 2", "description": "Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the CDKL5 gene." }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "CDKL5 early infantile epileptic encephalopathy", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "DEE2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "EIEE2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy, 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "early infantile epileptic encephalopathy caused by mutation in CDKL5", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "epileptic encephalopathy, early infantile, 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "epileptic encephalopathy, early infantile, type 2", "description": "" }, { "id": "MIM:300672", "resource": "MIM", "url": "https://www.omim.org/entry/300672", "name": "Developmental and epileptic encephalopathy 2", "description": "Developmental and epileptic encephalopathy 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "300672", "database": "MIM", "url": "https://www.omim.org/entry/300672" }, { "id": "0080467", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080467" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "479", "end_pos": "479" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "693", "end_pos": "693" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "788", "end_pos": "788" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "847", "end_pos": "847" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "919", "end_pos": "919" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O76039-2.512.512", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O76039-2.527.527", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O76039-2.543.543", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O76039-2.550.550", "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": 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": "O76039-2.543.543", "start_pos": 543, "end_pos": 543, "uniprot_canonical_ac": "O76039-2", "length": 960, "uniprot_id": "CDKL5_HUMAN", "protein_name": "Cyclin-dependent kinase-like 5", "refseq_ac": "NP_001032420", "refseq_name": "cyclin-dependent kinase-like 5 isoform 1", "gene_name": "CDKL5", "gene_names_uniprotkb": "CDKL5; STK9", "gene_names_refseq": "CDKL5; CFAP247; DEE2; EIEE2; ISSX; STK9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" } ], "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": "O76039", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76039" }, { "database": "O-GlcNAc Atlas", "id": "O76039", "url": "https://oglcnac.org/atlas/detail/O76039" } ], "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": "O76039", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76039", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "O76039", "url": "https://oglcnac.org/atlas/detail/O76039", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2147160942", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147160942", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLNSPTSPTPTRHSDTRTLL", "down_seq": "PSGRNNRNEGTLDSRRTTTR", "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": "Ser543", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "O76039", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76039" }, { "id": "O76039", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O76039" } ] } ], "snv": [ { "evidence": [ { "id": "rs2147160942", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147160942" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->X).", "chr_id": "X", "chr_pos": "18604552", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S543", "disease": [ { "disease_id": "DOID:0080467", "recommended_name": { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "developmental and epileptic encephalopathy 2", "description": "A developmental and epileptic encephalopathy characterized by X-linked dominant inheritance of seizure onset in the first months of life, intellectual disability, and poor motor control that has_material_basis_in mutation in the CDKL5 gene on chromosome Xp22." }, "synonyms": [ { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "X-linked infantile spasm syndrome 2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "DEE2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "EIEE2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "early infantile epileptic encephalopathy 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy, 2", "description": "Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the CDKL5 gene." }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "CDKL5 early infantile epileptic encephalopathy", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "DEE2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "EIEE2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy, 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "early infantile epileptic encephalopathy caused by mutation in CDKL5", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "epileptic encephalopathy, early infantile, 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "epileptic encephalopathy, early infantile, type 2", "description": "" }, { "id": "MIM:300672", "resource": "MIM", "url": "https://www.omim.org/entry/300672", "name": "Developmental and epileptic encephalopathy 2", "description": "Developmental and epileptic encephalopathy 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "300672", "database": "MIM", "url": "https://www.omim.org/entry/300672" }, { "id": "0080467", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080467" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "479", "end_pos": "479" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "693", "end_pos": "693" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "788", "end_pos": "788" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "847", "end_pos": "847" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "919", "end_pos": "919" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O76039-2.527.527", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O76039-2.531.531", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O76039-2.550.550", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O76039-2.559.559", "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": 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": "O76039-2.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "O76039-2", "length": 960, "uniprot_id": "CDKL5_HUMAN", "protein_name": "Cyclin-dependent kinase-like 5", "refseq_ac": "NP_001032420", "refseq_name": "cyclin-dependent kinase-like 5 isoform 1", "gene_name": "CDKL5", "gene_names_uniprotkb": "CDKL5; STK9", "gene_names_refseq": "CDKL5; CFAP247; DEE2; EIEE2; ISSX; STK9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2518776860", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2518776860", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "MKIPNIGNV", "down_seq": "NKFEILGVVGEGAYGVVLKC", "snv": [ { "evidence": [ { "id": "rs2518776860", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2518776860" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVM->NVT).", "chr_id": "X", "chr_pos": "18507125", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M10", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "479", "end_pos": "479" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "693", "end_pos": "693" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "788", "end_pos": "788" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "847", "end_pos": "847" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "919", "end_pos": "919" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O76039-2.6.6", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O76039-2.7.7", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O76039-2.13.13", "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": "O76039-2.131.131", "start_pos": 131, "end_pos": 131, "uniprot_canonical_ac": "O76039-2", "length": 960, "uniprot_id": "CDKL5_HUMAN", "protein_name": "Cyclin-dependent kinase-like 5", "refseq_ac": "NP_001032420", "refseq_name": "cyclin-dependent kinase-like 5 isoform 1", "gene_name": "CDKL5", "gene_names_uniprotkb": "CDKL5; STK9", "gene_names_refseq": "CDKL5; CFAP247; DEE2; EIEE2; ISSX; STK9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147142715", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147142715", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147142715", "url": "https://www.ensembl.org/id/rs2147142715", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KVKSYIYQLIKAIHWCHKND", "down_seq": "VHRDIKPENLLISHNDVLKL", "snv": [ { "evidence": [ { "id": "rs2147142715", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147142715" }, { "id": "rs2147142715", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147142715" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDI->NDT).", "chr_id": "X", "chr_pos": "18579957", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I131", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "479", "end_pos": "479" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "693", "end_pos": "693" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "788", "end_pos": "788" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "847", "end_pos": "847" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "919", "end_pos": "919" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "761", "end_pos": "761" } ] } ], "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": "O76039-2.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "O76039-2", "length": 960, "uniprot_id": "CDKL5_HUMAN", "protein_name": "Cyclin-dependent kinase-like 5", "refseq_ac": "NP_001032420", "refseq_name": "cyclin-dependent kinase-like 5 isoform 1", "gene_name": "CDKL5", "gene_names_uniprotkb": "CDKL5; STK9", "gene_names_refseq": "CDKL5; CFAP247; DEE2; EIEE2; ISSX; STK9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1922605766", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1922605766", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1922605766", "url": "https://www.ensembl.org/id/rs1922605766", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MKIPNIGNVMNK", "down_seq": "EILGVVGEGAYGVVLKCRHK", "snv": [ { "evidence": [ { "id": "rs1922605766", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1922605766" }, { "id": "rs1922605766", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1922605766" } ], "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": "X", "chr_pos": "18507134", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F13", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080467", "recommended_name": { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "developmental and epileptic encephalopathy 2", "description": "A developmental and epileptic encephalopathy characterized by X-linked dominant inheritance of seizure onset in the first months of life, intellectual disability, and poor motor control that has_material_basis_in mutation in the CDKL5 gene on chromosome Xp22." }, "synonyms": [ { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "X-linked infantile spasm syndrome 2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "DEE2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "EIEE2", "description": "" }, { "id": "DOID:0080467", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080467", "name": "early infantile epileptic encephalopathy 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy, 2", "description": "Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the CDKL5 gene." }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "CDKL5 early infantile epileptic encephalopathy", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "DEE2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "EIEE2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "developmental and epileptic encephalopathy, 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "early infantile epileptic encephalopathy caused by mutation in CDKL5", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "epileptic encephalopathy, early infantile, 2", "description": "" }, { "id": "MONDO:0010396", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010396", "name": "epileptic encephalopathy, early infantile, type 2", "description": "" }, { "id": "MIM:300672", "resource": "MIM", "url": "https://www.omim.org/entry/300672", "name": "Developmental and epileptic encephalopathy 2", "description": "Developmental and epileptic encephalopathy 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "300672", "database": "MIM", "url": "https://www.omim.org/entry/300672" }, { "id": "0080467", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080467" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "479", "end_pos": "479" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "693", "end_pos": "693" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "788", "end_pos": "788" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "847", "end_pos": "847" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "919", "end_pos": "919" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O76039-2.6.6", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O76039-2.7.7", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O76039-2.10.10", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "O76039-2.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "O76039-2", "length": 960, "uniprot_id": "CDKL5_HUMAN", "protein_name": "Cyclin-dependent kinase-like 5", "refseq_ac": "NP_001032420", "refseq_name": "cyclin-dependent kinase-like 5 isoform 1", "gene_name": "CDKL5", "gene_names_uniprotkb": "CDKL5; STK9", "gene_names_refseq": "CDKL5; CFAP247; DEE2; EIEE2; ISSX; STK9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147145524", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147145524", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147145524", "url": "https://www.ensembl.org/id/rs2147145524", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NDVLKLCDFGFARNLSEGNN", "down_seq": "NYTEYVATRWYRSPELLLGA", "snv": [ { "evidence": [ { "id": "rs2147145524", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147145524" }, { "id": "rs2147145524", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147145524" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNA->NNT).", "chr_id": "X", "chr_pos": "18584295", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A166", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "479", "end_pos": "479" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "693", "end_pos": "693" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "788", "end_pos": "788" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "847", "end_pos": "847" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "919", "end_pos": "919" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O76039-2.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O76039-2.178.178", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76039-2.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "O76039-2", "length": 960, "uniprot_id": "CDKL5_HUMAN", "protein_name": "Cyclin-dependent kinase-like 5", "refseq_ac": "NP_001032420", "refseq_name": "cyclin-dependent kinase-like 5 isoform 1", "gene_name": "CDKL5", "gene_names_uniprotkb": "CDKL5; STK9", "gene_names_refseq": "CDKL5; CFAP247; DEE2; EIEE2; ISSX; STK9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76039", "url": "https://www.uniprot.org/uniprotkb/O76039" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76039", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76039", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RNLSEGNNANYTEYVATRWY", "down_seq": "SPELLLGAPYGKSVDMWSVG", "snv": [ { "evidence": [ { "id": "O76039", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76039" } ], "glycoeffect": [], "subjects_tested": "1773", "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": "18584332", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R178", "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": "479", "end_pos": "479" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" } ] }, { "type": "snv", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "693", "end_pos": "693" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "788", "end_pos": "788" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "847", "end_pos": "847" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "919", "end_pos": "919" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O76039-2.166.166", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O76039-2.171.171", "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": [] } ] } ]