{ "uniprot_canonical_ac": "A1A4Y4-1", "ptm_annotation": [], "sequence": { "header": "sp|A1A4Y4-1|IRGM_HUMAN Isoform 1 of Immunity-related GTPase family M protein OS=Homo sapiens OX=9606 GN=IRGM PE=1 SV=2 CANONICAL=A1A4Y4-1", "length": 181, "sequence": "MEAMNVEKASADGNLPEVISNIKETLKIVSRTPVNITMAGDSGNGMSTFISALRNTGHEGKASPPTELVKATQRCASYFSSHFSNVVLWDLPGTGSATTTLENYLMEMQFNRYDFIMVASAQFSMNHVMLAKTAEDMGKKFYIVWTKLDMDLSTGALPEVQLLQIRENVLENLQKERVCEY" }, "uniprot_id": "IRGM_HUMAN", "enzyme_annotation": [ { "ec": "3.6.5.-", "activity": "" } ], "glycation": [], "keywords": [], "species": [ { "common_name": "Human", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "Homo sapiens", "taxid": 9606 } ], "publication": [ { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/14576437", "type": [ "PubMed" ], "id": "14576437" } ], "title": "Immune control of tuberculosis by IFN-gamma-inducible LRG-47.", "journal": "Science (New York, N.Y.)", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ], "authors": "MacMicking JD, Taylor GA, McKinney JD", "date": "2003" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/16277747", "type": [ "PubMed" ], "id": "16277747" } ], "title": "The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage.", "journal": "Genome Biol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "authors": "Dunn D.M., Leptin M., Bekpen C., Glowalla E., Guethlein L., Howard J.C., Hunn J.P., Parvanova I., Rohde C.", "date": "2005" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/16888103", "type": [ "PubMed" ], "id": "16888103" } ], "title": "Human IRGM induces autophagy to eliminate intracellular mycobacteria.", "journal": "Science", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" }, { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ], "authors": "Deretic V., Davis A.S., Singh S.B., Taylor G.A.", "date": "2006" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/17554261", "type": [ "PubMed" ], "id": "17554261" } ], "title": "Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.", "journal": "Nat. Genet.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" }, { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ], "authors": "Bethel G., Deloukas P., Bagnall R., Fisher S.A., Forbes A., Lewis C.M., Mansfield J.C., Mathew C.G., Onnie C.M., Prescott N.J., Sanderson J., Soars D., Barrett J.C., McArdle W., Roberts R.G., Jewell D.P., Ahmad T., Anderson C.A., Bryan C., Burke D.A., Cardon L., Cummings F.R., Drummond H., Khawaja S.A., Lees C.W., Nimmo E.R., Parkes M., Satsangi J., Strachan D., Todhunter C.E., Tremelling M.", "date": "2007" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/17921695", "type": [ "PubMed" ], "id": "17921695" } ], "title": "Genome-wide association scanning highlights two autophagy genes, ATG16L1 and IRGM, as being significantly associated with Crohn's disease.", "journal": "Autophagy", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ], "authors": "Massey DC, Parkes M", "date": "2007" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/19174780", "type": [ "PubMed" ], "id": "19174780" } ], "title": "Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort.", "journal": "Am. J. Gastroenterol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "authors": "Franke A., Schreiber S., Dijkstra G., Nolte I.M., Weersma R.K., Wijmenga C., Stokkers P.C., Cleynen I., Henckaerts L., Rutgeerts P., Vermeire S., Wolfkamp S.C.", "date": "2009" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/19266026", "type": [ "PubMed" ], "id": "19266026" } ], "title": "Death and resurrection of the human IRGM gene.", "journal": "PLoS Genet.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "authors": "Eichler E.E., Ventura M., Antonacci F., Alkan C., Marques-Bonet T., Bekpen C., Howard J.C., Kidd J.M., Leogrande M.B., Siswara P.", "date": "2009" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/20737271", "type": [ "PubMed" ], "id": "20737271" } ], "title": "Human IRGM gene `to be or not to be`.", "journal": "Seminars in immunopathology", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ], "authors": "Bekpen C, Xavier RJ, Eichler EE", "date": "2010" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/21278745", "type": [ "PubMed" ], "id": "21278745" } ], "title": "A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease.", "journal": "Nat. Genet.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "authors": "Barbry P., Harel-Bellan A., Souidi M., Brest P., Cesaro A., Darfeuille-Michaud A., Hebuterne X., Hofman P., Lapaquette P., Lebrigand K., Mari B., Mograbi B., Mosnier J.F., Vouret-Craviari V.", "date": "2011" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/30612879", "type": [ "PubMed" ], "id": "30612879" } ], "title": "The Crohn's Disease Risk Factor IRGM Limits NLRP3 Inflammasome Activation by Impeding Its Assembly and by Mediating Its Selective Autophagy.", "journal": "Molecular cell", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ], "authors": "Mehto S, Jena KK, Nath P, Chauhan S, Kolapalli SP, Das SK, Sahoo PK, Jain A, Taylor GA, Chauhan S", "date": "2019" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/31654602", "type": [ "PubMed" ], "id": "31654602" } ], "title": "Genetic polymorphisms of ATG16L1 and IRGM genes in Malaysian patients with Crohn's disease.", "journal": "Journal of digestive diseases", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ], "authors": "Kee BP, Ng JG, Ng CC, Hilmi I, Goh KL, Chua KH", "date": "2020" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/32045400", "type": [ "PubMed" ], "id": "32045400" } ], "title": "Clinical and Genetic Factors Associated With Complications After Crohn's Ileocolectomy.", "journal": "Diseases of the colon and rectum", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ], "authors": "Kline BP, Weaver T, Brinton DL Jr, Deiling S, Yochum GS, Berg AS, Koltun WA", "date": "2020" } ], "uniprot_ac": "A1A4Y4", "site_annotation": [ { "end_pos": 37, "annotation": "n_glycosylation_sequon", "start_pos": 35 } ], "isoforms": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4#A1A4Y4-1", "isoform_ac": "A1A4Y4-1", "locus": { "end_pos": 150848124, "strand": "-", "start_pos": 150848666, "chromosome": "5", "evidence": [ { "url": "https://www.ensembl.org/id/ENST00000522154", "id": "ENST00000522154", "database": "Ensembl Transcript" }, { "url": "https://www.ensembl.org/id/ENSP00000428220", "id": "ENSP00000428220", "database": "Ensembl Peptide" } ] }, "sequence": { "header": "sp|A1A4Y4-1|IRGM_HUMAN Isoform 1 of Immunity-related GTPase family M protein OS=Homo sapiens OX=9606 GN=IRGM PE=1 SV=2 CANONICAL=A1A4Y4-1", "length": 181, "sequence": "MEAMNVEKASADGNLPEVISNIKETLKIVSRTPVNITMAGDSGNGMSTFISALRNTGHEGKASPPTELVKATQRCASYFSSHFSNVVLWDLPGTGSATTTLENYLMEMQFNRYDFIMVASAQFSMNHVMLAKTAEDMGKKFYIVWTKLDMDLSTGALPEVQLLQIRENVLENLQKERVCEY" } }, { "url": "https://www.uniprot.org/uniprot/A1A4Y4#H0YBM2-1", "isoform_ac": "H0YBM2-1", "locus": { "end_pos": 150848497, "strand": "-", "start_pos": 150878034, "chromosome": "5", "evidence": [ { "url": "https://www.ensembl.org/id/ENST00000520549", "id": "ENST00000520549", "database": "Ensembl Transcript" }, { "url": "https://www.ensembl.org/id/ENSP00000429819", "id": "ENSP00000429819", "database": "Ensembl Peptide" } ] }, "sequence": { "header": "tr|H0YBM2-1|IRGM_HUMAN Computationally mapped isoform of Immunity-related GTPase family M protein OS=Homo sapiens OX=9606 GN=IRGM PE=1 SV=1 CANONICAL=A1A4Y4-1", "length": 71, "sequence": "XNHVMLAKTAEDMGKKFYIVWTKLDMDLSTGALPEVQLLQIRENVLENLQKERSSRNQQVYPNHSHVPLAC" } } ], "pathway": [ { "url": "https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+hsa:345611", "resource": "KEGG Pathway", "id": "hsa:345611", "name": "" } ], "function": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "annotation": "Genetic evidence implicates IRGM defects in the early immune response in individuals with Crohn's disease.", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ] }, { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "annotation": "Genetic polymorphisms of ATG16L1 and IRGM genes in Malaysian patients with Crohn's disease.", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ] }, { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "annotation": "IRGM inhibits NLRP3 inflammasome activation to keep colonic inflammation under check.", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ] }, { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "annotation": "IRGM is significantly associated with Crohn disease.", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ] }, { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "annotation": "Identified a function for IRGM in the control of intracellular pathogens and report that IRGM plays a role in autophagy and in the reduction of intracellular Mycobacterium var. bovis BCG load", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ] }, { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "annotation": "In addition to clinical risk factors, the rs13361189 single nucleotide polymorphism in the IRGM gene was independently associated with complications after ileocolectomy for Crohn's disease.", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ] }, { "url": "https://www.uniprot.org/uniprot/A1A4Y4#function", "annotation": "Putative GTPase which is required for clearance of acute protozoan and bacterial infections. Functions in innate immune response probably through regulation of autophagy. May regulate proinflammatory cytokine production and prevent endotoxemia upon infection. May also play a role in macrophages adhesion and motility (By similarity).", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4#function", "id": "A1A4Y4", "database": "UniProtKB" } ] }, { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "annotation": "The unusual evolutionary history of the IRGM locus and the important role of the IRGM gene in autophagy and Crohn's disease in response to pathogenesis. Review article", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "id": "NP_001139277.1", "database": "RefSeq" } ] } ], "orthologs": [], "interactions": [], "synthesized_glycans": [], "snv": [ { "sequence_org": "F", "start_pos": 141, "alt_nt": "A", "chr_id": "5", "ref_nt": "T", "chr_pos": "150228106", "disease": [ { "synonyms": [ { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "malignant hematopoietic neoplasm", "description": "" } ], "recommended_name": { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "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." } } ], "evidence": [ { "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/A1A4Y4", "id": "A1A4Y4", "database": "BioMuta" } ], "glycoeffect": [], "frequency": "2.1", "sequence_mut": "I", "subjects_tested": "48", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "annotation": "Somatic mutation passed 1 out of 6 filters: patient freq. (2.1%).", "end_pos": 141, "minor_allelic_frequency": "", "subjects_positive": "1" }, { "sequence_org": "T", "start_pos": 94, "alt_nt": "A", "chr_id": "5", "ref_nt": "C", "chr_pos": "150227966", "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/A1A4Y4", "id": "A1A4Y4", "database": "BioMuta" } ], "glycoeffect": [ "o-glyco-site-loss" ], "frequency": "1.5", "sequence_mut": "K", "subjects_tested": "66", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "annotation": "Somatic mutation passed 1 out of 6 filters: patient freq. (1.5%).", "end_pos": 94, "minor_allelic_frequency": "", "subjects_positive": "1" } ], "cluster_types": [ { "name": "isoformset.uniprotkb", "label": "Isoforms" } ], "refseq": { "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001139277.1", "ac": "NP_001139277.1", "name": "immunity-related GTPase family M protein isoform 2", "summary": "This gene encodes a member of the p47 immunity-related GTPase family. The encoded protein may play a role in the innate immune response by regulating autophagy formation in response to intracellular pathogens. Polymorphisms that affect the normal expression of this gene are associated with a susceptibility to Crohn's disease and tuberculosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2016]." }, "go_annotation": { "categories": [ { "go_terms": [ { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0003924", "pmid": "21873635", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "GTPase activity", "id": "GO:0003924" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0019901", "pmid": "25891078", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "protein kinase binding", "id": "GO:0019901" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0043539", "pmid": "28389568", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "protein serine/threonine kinase activator activity", "id": "GO:0043539" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0051434", "pmid": "25891078", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "BH3 domain binding", "id": "GO:0051434" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0050700", "pmid": "25891078", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "CARD domain binding", "id": "GO:0050700" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005525", "pmid": "", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "GTP binding", "id": "GO:0005525" } ], "total": 6, "name": "Molecular Function" }, { "go_terms": [ { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0000139", "pmid": "28389568", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "Golgi membrane", "id": "GO:0000139" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005739", "pmid": "25891078", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "mitochondrion", "id": "GO:0005739" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005739", "pmid": "28389568", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "mitochondrion", "id": "GO:0005739" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005794", "pmid": "28389568", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "Golgi apparatus", "id": "GO:0005794" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005829", "pmid": "25891078", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "cytosol", "id": "GO:0005829" }, { "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005789", "pmid": "21873635", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A1A4Y4", "id": "A1A4Y4", "database": "UniProtKB" } ], "name": "endoplasmic 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