{ "uniprot_canonical_ac": "A0A0A0MS05-1", "ptm_annotation": [], "sequence": { "header": "sp|A0A0A0MS05-1|TVB57_HUMAN Isoform 1 of Probable non-functional T cell receptor beta variable 5-7 OS=Homo sapiens OX=9606 GN=TRBV5-7 PE=1 SV=1 CANONICAL=A0A0A0MS05-1", "length": 114, "sequence": "MGPGLLCWVLLCPLGEGPVDAGVTQSPTHLIKTRGQHVTLRCSPISGHTSVSSYQQALGQGPQFIFQYYEKEERGRGNFPDQFSGHQFPNYSSELNVNALLLGDSALYLCASSL" }, "uniprot_id": "TVB57_HUMAN", "enzyme_annotation": [], "glycation": [], "keywords": [ "glycoprotein", "predicted.uniprotkb_gly" ], "species": [ { "common_name": "Human", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05", "id": "A0A0A0MS05", "database": "UniProtKB" } ], "name": "Homo sapiens", "taxid": 9606 } ], "publication": [ { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/15040585", "type": [ "PubMed" ], "id": "15040585" } ], "title": "The many important facets of T-cell repertoire diversity.", "journal": "Nat. Rev. Immunol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05", "id": "A0A0A0MS05", "database": "UniProtKB" } ], "authors": "Messaoudi I., Nikolich-Zugich J., Slifka M.K.", "date": "2004" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/20452950", "type": [ "PubMed" ], "id": "20452950" } ], "title": "Structural biology of the T-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling.", "journal": "Cold Spring Harb. Perspect. Biol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05", "id": "A0A0A0MS05", "database": "UniProtKB" } ], "authors": "Gagnon E., Wucherpfennig K.W., Call M.E., Call M.J., Huseby E.S.", "date": "2010" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/23524462", "type": [ "PubMed" ], "id": "23524462" } ], "title": "T cell receptor signalling networks: branched, diversified and bounded.", "journal": "Nat. Rev. Immunol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05", "id": "A0A0A0MS05", "database": "UniProtKB" } ], "authors": "Zamoyska R., Brownlie R.J.", "date": "2013" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/24600447", "type": [ "PubMed" ], "id": "24600447" } ], "title": "Immunoglobulin and T Cell Receptor Genes: IMGT((R)) and the Birth and Rise of Immunoinformatics.", "journal": "Front. Immunol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05", "id": "A0A0A0MS05", "database": "UniProtKB" } ], "authors": "Lefranc M.P.", "date": "2014" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/25493333", "type": [ "PubMed" ], "id": "25493333" } ], "title": "T cell antigen receptor recognition of antigen-presenting molecules.", "journal": "Annu. Rev. Immunol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05", "id": "A0A0A0MS05", "database": "UniProtKB" } ], "authors": "Rossjohn J., Gras S., McCluskey J., Godfrey D.I., Miles J.J., Turner S.J.", "date": "2015" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/9619395", "type": [ "PubMed" ], "id": "9619395" } ], "title": "IMGT (ImMunoGeneTics) locus on focus. A new section of Experimental and Clinical Immunogenetics.", "journal": "Exp. Clin. Immunogenet.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05", "id": "A0A0A0MS05", "database": "UniProtKB" } ], "authors": "Lefranc M.P.", "date": "1998" } ], "uniprot_ac": "A0A0A0MS05", "site_annotation": [ { "end_pos": 92, "annotation": "n_glycosylation_sequon", "start_pos": 90 } ], "isoforms": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05#A0A0A0MS05-1", "isoform_ac": "A0A0A0MS05-1", "locus": { "end_pos": 142520090, "strand": "-", "start_pos": 142520555, "chromosome": "7", "evidence": [ { "url": "https://www.ensembl.org/id/ENST00000390378", "id": "ENST00000390378", "database": "Ensembl Transcript" }, { "url": "https://www.ensembl.org/id/ENSP00000374901", "id": "ENSP00000374901", "database": "Ensembl Peptide" } ] }, "sequence": { "header": "sp|A0A0A0MS05-1|TVB57_HUMAN Isoform 1 of Probable non-functional T cell receptor beta variable 5-7 OS=Homo sapiens OX=9606 GN=TRBV5-7 PE=1 SV=1 CANONICAL=A0A0A0MS05-1", "length": 114, "sequence": "MGPGLLCWVLLCPLGEGPVDAGVTQSPTHLIKTRGQHVTLRCSPISGHTSVSSYQQALGQGPQFIFQYYEKEERGRGNFPDQFSGHQFPNYSSELNVNALLLGDSALYLCASSL" } } ], "pathway": [], "function": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05#function", "annotation": "Probable non-functional open reading frame (ORF) of V region of the variable domain of T cell receptor (TR) beta chain (PubMed:24600447). Non-functional ORF generally cannot participate to the synthesis of a productive T cell receptor (TR) chain due to altered V-(D)-J or switch recombination and/or splicing site (at mRNA level) and/or conserved amino acid change (protein level) (PubMed:9619395). Alpha-beta T cell receptors are antigen specific receptors which are essential to the immune response and are present on the cell surface of T lymphocytes. Recognize peptide-major histocompatibility (MH) (pMH) complexes that are displayed by antigen presenting cells (APC), a prerequisite for efficient T cell adaptive immunity against pathogens (PubMed:25493333). Binding of alpha-beta TR to pMH complex initiates TR-CD3 clustering on the cell surface and intracellular activation of LCK that phosphorylates the ITAM motifs of CD3G, CD3D, CD3E and CD247 enabling the recruitment of ZAP70. In turn ZAP70 phosphorylates LAT, which recruits numerous signaling molecules to form the LAT signalosome. The LAT signalosome propagates signal branching to three major signaling pathways, the calcium, the mitogen-activated protein kinase (MAPK) kinase and the nuclear factor NF-kappa-B (NF-kB) pathways, leading to the mobilization of transcription factors that are critical for gene expression and essential for T cell growth and differentiation (PubMed:23524462). The T cell repertoire is generated in the thymus, by V-(D)-J rearrangement. This repertoire is then shaped by intrathymic selection events to generate a peripheral T cell pool of self-MH restricted, non-autoaggressive T cells. Post-thymic interaction of alpha-beta TR with the pMH complexes shapes TR structural and functional avidity (PubMed:15040585).", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A0A0MS05#function", "id": "A0A0A0MS05", "database": "UniProtKB" } ] } ], "orthologs": [], "interactions": [], "synthesized_glycans": [], "snv": [ { "sequence_org": "T", "start_pos": 49, "alt_nt": "T", "chr_id": "7", "ref_nt": "G", "chr_pos": "142111590", "disease": [ { "synonyms": [], "recommended_name": { "id": "DOID:1324", "url": "http://disease-ontology.org/term/DOID:1324", "resource": "Disease Ontology", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." } } ], "evidence": [ { "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/A0A0A0MS05", "id": "A0A0A0MS05", "database": "BioMuta" } ], "glycoeffect": [ "o-glyco-site-loss" ], "frequency": "1.2", "sequence_mut": "N", "subjects_tested": "1514", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "annotation": "Somatic mutation passed 2 out of 6 filters: patient freq. 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(2.0%); patient count (30/1514).", "end_pos": 49, "minor_allelic_frequency": "", "subjects_positive": "30" }, { "sequence_org": "T", "alt_nt": "null", "chr_id": "7", "ref_nt": "A", "chr_pos": "142520284C>", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371384757", "id": "rs371384757", "database": "dbSNP" }, { "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371384757", "id": "rs371384757", "database": "ExAC" }, { "url": "https://www.ncbi.nlm.nih.gov/snp/rs371384757#frequency_tab", "id": "rs371384757", "database": "TOPMed" }, { "url": "http://gnomad.broadinstitute.org/awesome?query=rs371384757", "id": "rs371384757", "database": "gnomAD" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_mut": "N", "start_pos": 24, "keywords": [ "ebi", "germline" ], "end_pos": 24, "minor_allelic_frequency": "", "annotation": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (TQS->NQS)." }, { "sequence_org": "H", "start_pos": 37, "alt_nt": "G", "chr_id": "7", "ref_nt": "T", "chr_pos": "142111626", "disease": [ { "synonyms": [ { "id": "DOID:2394", "url": "http://disease-ontology.org/term/DOID:2394", "resource": "Disease Ontology", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "url": "http://disease-ontology.org/term/DOID:2394", "resource": "Disease Ontology", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "url": "http://disease-ontology.org/term/DOID:2394", "resource": "Disease Ontology", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "url": "http://disease-ontology.org/term/DOID:2394", "resource": "Disease Ontology", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "url": "http://disease-ontology.org/term/DOID:2394", "resource": "Disease Ontology", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "url": "http://disease-ontology.org/term/DOID:2394", "resource": "Disease Ontology", "name": "tumor of the Ovary", "description": "" } ], "recommended_name": { "id": "DOID:2394", "url": "http://disease-ontology.org/term/DOID:2394", "resource": "Disease Ontology", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." } } ], "evidence": [ { "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/A0A0A0MS05", "id": "A0A0A0MS05", "database": "BioMuta" } ], "glycoeffect": [], "frequency": "1.1", "sequence_mut": "P", "subjects_tested": "93", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "annotation": "Somatic mutation passed 1 out of 6 filters: patient freq. (1.1%).", "end_pos": 37, "minor_allelic_frequency": "", "subjects_positive": "1" }, { "sequence_org": "H", "start_pos": 37, "alt_nt": "T", "chr_id": "7", "ref_nt": "G", "chr_pos": "142111625", "disease": [ { "synonyms": [ { "id": "DOID:10534", "url": "http://disease-ontology.org/term/DOID:10534", "resource": "Disease Ontology", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "url": "http://disease-ontology.org/term/DOID:10534", "resource": "Disease Ontology", "name": "gastric neoplasm", "description": "" } ], "recommended_name": { "id": "DOID:10534", "url": "http://disease-ontology.org/term/DOID:10534", "resource": "Disease Ontology", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." } }, { "synonyms": [ { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "pancreatic tumor", "description": "" } ], "recommended_name": { "id": "DOID:1793", "url": "http://disease-ontology.org/term/DOID:1793", "resource": "Disease Ontology", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." } }, { "synonyms": [ { "id": "DOID:1612", "url": "http://disease-ontology.org/term/DOID:1612", "resource": "Disease Ontology", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "url": "http://disease-ontology.org/term/DOID:1612", "resource": "Disease Ontology", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "url": "http://disease-ontology.org/term/DOID:1612", "resource": "Disease Ontology", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "url": "http://disease-ontology.org/term/DOID:1612", "resource": "Disease Ontology", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "url": "http://disease-ontology.org/term/DOID:1612", "resource": "Disease Ontology", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "url": "http://disease-ontology.org/term/DOID:1612", "resource": "Disease Ontology", "name": "primary breast cancer", "description": "" } ], "recommended_name": { "id": "DOID:1612", "url": "http://disease-ontology.org/term/DOID:1612", "resource": "Disease Ontology", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland." } }, { "synonyms": [ { "id": "DOID:11934", "url": "http://disease-ontology.org/term/DOID:11934", "resource": "Disease Ontology", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "url": "http://disease-ontology.org/term/DOID:11934", "resource": "Disease Ontology", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "url": "http://disease-ontology.org/term/DOID:11934", "resource": "Disease Ontology", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "url": "http://disease-ontology.org/term/DOID:11934", "resource": "Disease Ontology", "name": "tumor of head and neck", "description": "" } ], "recommended_name": { "id": "DOID:11934", "url": "http://disease-ontology.org/term/DOID:11934", "resource": "Disease Ontology", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. 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