Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	345611
Gene name	Immunity related GTPase M
Gene symbol	IRGM
Synonyms (NCBI Gene)	IBD19IFI1IRGM1LRG-47LRG47
Chromosome	5
Chromosome location	5q33.1
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 expressi

Show/Hide all (1)

SNP ID	Visualize variation	Clinical significance	Consequence
rs10065172	C>A,T	Pathogenic	Missense variant, synonymous variant, coding sequence variant

Show/Hide all (97)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000045	Process	Autophagosome assembly	IBA
GO:0000045	Process	Autophagosome assembly	IDA	28890335
GO:0000045	Process	Autophagosome assembly	IMP	16888103
GO:0000139	Component	Golgi membrane	IDA	28389568
GO:0000139	Component	Golgi membrane	IEA
GO:0000166	Function	Nucleotide binding	IEA
GO:0000421	Component	Autophagosome membrane	IDA	30612879
GO:0000421	Component	Autophagosome membrane	IEA
GO:0001891	Component	Phagocytic cup	IEA
GO:0001934	Process	Positive regulation of protein phosphorylation	IMP	28389568
GO:0002376	Process	Immune system process	IEA
GO:0003924	Function	GTPase activity	IBA
GO:0003924	Function	GTPase activity	IDA	29420192
GO:0003924	Function	GTPase activity	IEA
GO:0003925	Function	G protein activity	IDA	30612879
GO:0005515	Function	Protein binding	IPI	25891078, 32814053
GO:0005525	Function	GTP binding	IEA
GO:0005739	Component	Mitochondrion	IDA	21102437
GO:0005739	Component	Mitochondrion	IDA	25891078, 28389568
GO:0005739	Component	Mitochondrion	IEA
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005765	Component	Lysosomal membrane	ISS
GO:0005768	Component	Endosome	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0005794	Component	Golgi apparatus	IDA	28389568
GO:0005794	Component	Golgi apparatus	IEA
GO:0005829	Component	Cytosol	IDA	25891078
GO:0005886	Component	Plasma membrane	IEA
GO:0006914	Process	Autophagy	IDA	25891078
GO:0006914	Process	Autophagy	IEA
GO:0006954	Process	Inflammatory response	IEA
GO:0007040	Process	Lysosome organization	IDA	32753672, 35662396
GO:0010508	Process	Positive regulation of autophagy	IDA	25891078
GO:0010508	Process	Positive regulation of autophagy	IDA	25891078, 29420192
GO:0010508	Process	Positive regulation of autophagy	IMP	16888103, 25891078, 28389568
GO:0010800	Process	Positive regulation of peptidyl-threonine phosphorylation	IMP	25891078
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0019901	Function	Protein kinase binding	IPI	25891078
GO:0030163	Process	Protein catabolic process	IDA	30612879, 32715615, 36221902
GO:0030670	Component	Phagocytic vesicle membrane	IEA
GO:0030674	Function	Protein-macromolecule adaptor activity	IDA	25891078, 29420192, 30612879, 32715615, 32753672, 36221902
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031648	Process	Protein destabilization	IMP	25891078
GO:0031902	Component	Late endosome membrane	IEA
GO:0031966	Component	Mitochondrial membrane	IEA
GO:0031966	Component	Mitochondrial membrane	ISS
GO:0032480	Process	Negative regulation of type I interferon production	IDA	32715615, 34467632
GO:0032689	Process	Negative regulation of type II interferon production	ISS
GO:0033138	Process	Positive regulation of peptidyl-serine phosphorylation	IMP	25891078
GO:0035458	Process	Cellular response to interferon-beta	IBA
GO:0042742	Process	Defense response to bacterium	IDA	25891078
GO:0042742	Process	Defense response to bacterium	IDA	25891078, 32753672, 32939830
GO:0042742	Process	Defense response to bacterium	IMP	16888103, 19165925
GO:0042995	Component	Cell projection	IEA
GO:0043032	Process	Positive regulation of macrophage activation	ISS
GO:0043124	Process	Negative regulation of canonical NF-kappaB signal transduction	IDA	36221902
GO:0043254	Process	Regulation of protein-containing complex assembly	IMP	25891078
GO:0043539	Function	Protein serine/threonine kinase activator activity	IDA	25891078
GO:0043539	Function	Protein serine/threonine kinase activator activity	IMP	28389568
GO:0044546	Process	NLRP3 inflammasome complex assembly	IDA	35114687, 35254907
GO:0045087	Process	Innate immune response	IBA
GO:0045087	Process	Innate immune response	IEA
GO:0045087	Process	Innate immune response	IMP	16888103
GO:0045824	Process	Negative regulation of innate immune response	IDA	35662396
GO:0050687	Process	Negative regulation of defense response to virus	IDA	34467632, 36221902
GO:0050700	Function	CARD domain binding	IMP	25891078
GO:0050728	Process	Negative regulation of inflammatory response	IDA	30612879
GO:0050821	Process	Protein stabilization	IMP	25891078
GO:0050829	Process	Defense response to Gram-negative bacterium	IMP	25891078
GO:0051434	Function	BH3 domain binding	IMP	25891078
GO:0060335	Process	Positive regulation of type II interferon-mediated signaling pathway	IMP	16888103
GO:0061635	Process	Regulation of protein complex stability	IMP	25891078
GO:0061739	Process	Protein lipidation involved in autophagosome assembly	IMP	28389568
GO:0061762	Process	CAMKK-AMPK signaling cascade	IMP	25891078
GO:0065003	Process	Protein-containing complex assembly	IDA	25891078
GO:0065003	Process	Protein-containing complex assembly	IDA	25891078
GO:0070431	Process	Nucleotide-binding oligomerization domain containing 2 signaling pathway	IMP	25891078
GO:0071211	Process	Protein targeting to vacuole involved in autophagy	IDA	36221902
GO:0071211	Process	Protein targeting to vacuole involved in autophagy	IDA	29420192
GO:0071222	Process	Cellular response to lipopolysaccharide	IMP	25891078
GO:0071902	Process	Positive regulation of protein serine/threonine kinase activity	IMP	28389568
GO:0090141	Process	Positive regulation of mitochondrial fission	IDA	21102437
GO:0097352	Process	Autophagosome maturation	ISS
GO:0098586	Process	Cellular response to virus	IMP	28389568
GO:0140367	Process	Antibacterial innate immune response	IDA	32753672, 35662396
GO:0160049	Process	Negative regulation of cGAS/STING signaling pathway	IDA	32715615
GO:1900181	Process	Negative regulation of protein localization to nucleus	IDA	35662396
GO:1900182	Process	Positive regulation of protein localization to nucleus	IDA	25720963, 32753672
GO:1900226	Process	Negative regulation of NLRP3 inflammasome complex assembly	IDA	30612879
GO:1901098	Process	Positive regulation of autophagosome maturation	IMP	16888103
GO:1901526	Process	Positive regulation of mitophagy	IDA	21102437, 32939830
GO:1901612	Function	Cardiolipin binding	IDA	21102437
GO:1904417	Process	Positive regulation of xenophagy	IDA	25891078
GO:1905673	Process	Positive regulation of lysosome organization	IDA	25720963
GO:1905673	Process	Positive regulation of lysosome organization	IDA	32753672

MIM	HGNC	e!Ensembl
608212	29597	ENSG00000237693

A1A4Y4

Protein name

Immunity-related GTPase family M protein (EC 3.6.5.-) (Immunity-related GTPase family M protein 1) (Interferon-inducible protein 1) (LPS-stimulated RAW 264.7 macrophage protein 47 homolog) (LRG-47)

Protein function

Immunity-related GTPase that plays important roles in innate immunity and inflammatory response (PubMed:16888103, PubMed:19165925, PubMed:25891078). Acts as a dynamin-like protein that binds to intracellular membranes and promotes remodeling and

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05049	IIGP	2 → 181	Interferon-inducible GTPase (IIGP)	Family

Tissue specificity

TISSUE SPECIFICITY: Widely expressed (at protein level) (PubMed:16888103). Expressed in several tissues including colon, small bowel and peripheral blood leukocytes (PubMed:17554261). {ECO:0000269|PubMed:16888103, ECO:0000269|PubMed:17554261}.

Sequence

MEAMNVEKASADGNLPEVISNIKETLKIVSRTPVNITMAGDSGNGMSTFISALRNTGHEG
KASPPTELVKATQRCASYFSSHFSNVVLWDLPGTGSATTTLENYLMEMQFNRYDFIMVAS
AQFSMNHVMLAKTAEDMGKKFYIVWTKLDMDLSTGALPEVQLLQIRENVLENLQKERVCE
Y

Sequence length

181

Interactions

View interactions

	KEGG
	NOD-like receptor signaling pathway Toxoplasmosis

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ANKYLOSING SPONDYLITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC LEFT-SIDED ULCERATIVE COLITIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLITIS, ULCERATIVE	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN DISEASE	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHNS DISEASE OF LARGE BOWEL	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Inflammatory bowel disease 19	Benign	ClinVar CTD, ClinVar, Disgenet CTD, ClinVar, Disgenet CTD, ClinVar, Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
INFLAMMATORY BOWEL DISEASES	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IRGM-related disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RHEUMATOID ARTHRITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCLEROSING CHOLANGITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TUBERCULOMA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (67)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Ankylosing spondylitis	Ankylosing Spondylitis	GWASCAT_DG	26974007		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ankylosing spondylitis	Ankylosing Spondylitis	BEFREE	28031552		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Arteriosclerosis	Arteriosclerosis	BEFREE	23689639, 27439214		★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	BEFREE	31654602		★★★★★ ★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	GWASDB_DG	21150878		★★★★★ ★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	BEFREE	23689639, 27439214		★★★★★ ★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	28814662		★★★★★ ★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	29992164	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Celiac Disease	Celiac disease	BEFREE	19683022		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholangitis, Sclerosing	Cholangitis	GWASCAT_DG	26974007		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colitis	Colitis	BEFREE	31177914		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colitis Ulcerative	Ulcerative colitis	Pubtator	23365659, 25191865	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colonic Diseases	Colonic disease	Pubtator	21830272, 23300620	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	BEFREE	17554261, 17921695, 18438406, 18726145, 18753178, 19000829, 19029815, 19098858, 19165925, 19491842, 19683022, 19802564, 19897957, 20360734, 20616747 View all (45 more)		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Crohn Disease	Crohn Disease	LHGDN	17554261, 17921695, 18580884		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Crohn Disease	Crohn Disease	CTD_human_DG	17554261, 18438406, 19165925, 21278745		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Crohn Disease	Crohn Disease	GWASCAT_DG	17554300, 18587394, 21102463, 26192919, 26974007, 28067908		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Crohn Disease	Crohn Disease	GWASDB_DG	17554300, 18587394, 21102463		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Crohn Disease	Crohn disease	Pubtator	18438406, 19165925, 20106866, 20117335, 20360734, 21049557, 21079743, 21283700, 21548950, 21830272, 22929019, 23365659, 25191865, 25891078, 26313894 View all (5 more)	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Crohn Disease	Crohn Disease	GENOMICS_ENGLAND_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Crohn`s disease of large bowel	Crohn`s Disease Of Large Bowel	CTD_human_DG	17554261, 18438406, 19165925, 21278745		★★★★★ ★☆☆☆☆ Found in Text Mining only
Crohn`s disease of the ileum	Crohn`s Disease Of The Ileum	CTD_human_DG	17554261, 18438406, 19165925, 21278745		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	37705061	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty Liver	BEFREE	30597691		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastroenteritis	Gastroenteritis	BEFREE	20616747		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastrointestinal inflammation	Gastrointestinal inflammation	BEFREE	29274870		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gaucher Disease	Gaucher disease	Pubtator	29992164	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	24859836, 30288851, 30391210		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	24859836	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	27439214		★★★★★ ★☆☆☆☆ Found in Text Mining only
Graves Disease	Graves disease	Pubtator	29992164	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Idiopathic pulmonary fibrosis	Pubtator	36578501	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
IIeocolitis	Ileocolitis	CTD_human_DG	17554261, 18438406, 19165925, 21278745		★★★★★ ★☆☆☆☆ Found in Text Mining only
Immunologic Deficiency Syndromes	Immunologic Deficiency Syndromes	BEFREE	23842753		★★★★★ ★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Disease 19	Inflammatory Bowel Disease	CTD_human_DG			★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Inflammatory Bowel Disease 19	Inflammatory Bowel Disease	CLINVAR_DG			★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Inflammatory Bowel Disease 19	Inflammatory Bowel Disease	GENOMICS_ENGLAND_DG			★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Inflammatory Bowel Diseases	Inflammatory bowel disease	Pubtator	18246054, 21049557, 25191865, 27802154, 27932194	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	18753178, 19491842, 19683022, 20177049, 21252204, 22065112, 22508677, 22955361, 23365659, 24232856, 25191865, 26066377, 28031552		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	GWASDB_DG	23128233		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	GWASCAT_DG	23128233, 28067908		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	CTD_human_DG	26192919		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Irritable Bowel Syndrome	Irritable Bowel Syndrome	BEFREE	28031552		★★★★★ ★☆☆☆☆ Found in Text Mining only
Language Disorders	Language Disorders	BEFREE	24859836		★★★★★ ★☆☆☆☆ Found in Text Mining only
Language Disorders	Language development disorders	Pubtator	24859836	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leprosy	Leprosy	BEFREE	24264476		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	29126912		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	30755075		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lupus Nephritis	Lupus Nephritis	BEFREE	30755075		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	22713085		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24859836		★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	BEFREE	20056715		★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	GWASDB_DG	22190364		★★★★★ ★☆☆☆☆ Found in Text Mining only
NON RARE IN EUROPE: Crohn disease	Crohn disease	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-alcoholic Fatty Liver Disease	Non-Alcoholic Fatty Liver Disease	BEFREE	29788077, 30597691		★★★★★ ★☆☆☆☆ Found in Text Mining only
Paratuberculosis	Paratuberculosis	BEFREE	18726145		★★★★★ ★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	GWASCAT_DG	26974007		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Regional enteritis	Crohn Disease	CTD_human_DG	17554261, 18438406, 19165925, 21278745		★★★★★ ★☆☆☆☆ Found in Text Mining only
Septicemia	Septicemia	BEFREE	24626347		★★★★★ ★☆☆☆☆ Found in Text Mining only
Steatohepatitis	Fatty Liver	BEFREE	30597691		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	22713085		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	25707354	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Thyroiditis Autoimmune	Thyroiditis	Pubtator	29992164	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ulcerative Colitis	Ulcerative colitis	BEFREE	19491842, 22065112, 22508677, 23365659, 25191865		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ulcerative Colitis	Ulcerative colitis	CTD_human_DG	20228799		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ulcerative Colitis	Ulcerative colitis	GWASCAT_DG	26192919, 26974007		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vasculitis	Vasculitis	Pubtator	34961976	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

IRGM (immunity related GTPase M)