IRGM immunity related GTPase M [Homo sapiens (human)] - Gene

Summary

Official Symbol: IRGMprovided by HGNC
Official Full Name: immunity related GTPase Mprovided by HGNC
Primary source: HGNC:HGNC:29597
See related: Ensembl:ENSG00000237693 MIM:608212; AllianceGenome:HGNC:29597
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: IFI1; IBD19; IRGM1; LRG47; LRG-47
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]
Expression: Low expression observed in reference dataset See more
Orthologs: all
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Genomic context

Location:: 5q33.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (150846521..150902402)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (151383019..151438900)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (150226083..150281964)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

IRGM is a novel regulator of PD-L1 via promoting S6K1-mediated phosphorylation of YBX1 in hepatocellular carcinoma.
Title: IRGM is a novel regulator of PD-L1 via promoting S6K1-mediated phosphorylation of YBX1 in hepatocellular carcinoma.
TAOK3 Facilitates Esophageal Squamous Cell Carcinoma Progression and Cisplatin Resistance Through Augmenting Autophagy Mediated by IRGM.
Title: TAOK3 Facilitates Esophageal Squamous Cell Carcinoma Progression and Cisplatin Resistance Through Augmenting Autophagy Mediated by IRGM.
Evaluation of Immunity-related GTPase Family M Protein (IRGM) SNPs among Egyptian Lupus Patients: A Case-control Study.
Title: Evaluation of Immunity-related GTPase Family M Protein (IRGM) SNPs among Egyptian Lupus Patients: A Case-control Study.
Race-specific association of an IRGM risk allele with cytokine expression in human subjects.
Title: Race-specific association of an IRGM risk allele with cytokine expression in human subjects.
Differential Requirement for IRGM Proteins during Tuberculosis Infection in Mice.
Title: Differential Requirement for IRGM Proteins during Tuberculosis Infection in Mice.
IRGM/Irgm1 deficiency inhibits neutrophil-platelet interactions and thrombosis in experimental atherosclerosis and arterial injury.
Title: IRGM/Irgm1 deficiency inhibits neutrophil-platelet interactions and thrombosis in experimental atherosclerosis and arterial injury.
Association of IRGM promoter region polymorphisms and haplotype with pulmonary tuberculosis in Pakistani (Punjab) population.
Title: Association of IRGM promoter region polymorphisms and haplotype with pulmonary tuberculosis in Pakistani (Punjab) population.
Association of IRGM gene promoter polymorphisms with hepatitis B virus infection.
Title: Association of IRGM gene promoter polymorphisms with hepatitis B virus infection.
IRGM/Irgm1 facilitates macrophage apoptosis through ROS generation and MAPK signal transduction: Irgm1 (+/-) mice display increases atherosclerotic plaque stability.
Title: IRGM/Irgm1 facilitates macrophage apoptosis through ROS generation and MAPK signal transduction: Irgm1(+/-) mice display increases atherosclerotic plaque stability.
Interferon-gamma activated T-cell IRGM-autophagy axis in oral lichen planus.
Title: Interferon-γ activated T-cell IRGM-autophagy axis in oral lichen planus.

Submit: New GeneRIF Correction See all GeneRIFs (85)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Inflammatory bowel disease 19 MedGen: C2677079 OMIM: 612278 GeneReviews: Not available	Compare labs
Mycobacterium tuberculosis, susceptibility to MedGen: C1834752 OMIM: 607948 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Depletion of IRGM reduces HIV-1-increased LC3-II expression. IRGM is involved in HIV-mediated autophagosome accumulation via its interaction with Nef	PubMed
	nef	Protein/protein interactions of virus/autophagy-associated proteins by yeast two-hybrid array reveals the interaction between HIV-1 Nef and immunity-related GTPase family M protein (IRGM)	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables BH3 domain binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables CARD domain binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables G protein activity	IDA Inferred from Direct Assay more info	PubMed
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein serine/threonine kinase activator activity	IDA Inferred from Direct Assay more info	PubMed
enables protein serine/threonine kinase activator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein-macromolecule adaptor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in CAMKK-AMPK signaling cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagosome assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagosome maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to interferon-beta	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to lipopolysaccharide	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in defense response to Gram-negative bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in defense response to bacterium	IDA Inferred from Direct Assay more info	PubMed
involved_in defense response to bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of NLRP3 inflammasome complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cGAS/STING signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of defense response to virus	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of type I interferon production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of type II interferon production	ISS Inferred from Sequence or Structural Similarity more info
involved_in nucleotide-binding oligomerization domain containing 2 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of autophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of lysosome organization	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of macrophage activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of mitophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of peptidyl-serine phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of peptidyl-threonine phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein serine/threonine kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of type II interferon-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of xenophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in protein destabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein lipidation involved in autophagosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to vacuole involved in autophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in protein-containing complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of protein complex stability	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein-containing complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in autophagosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in mitochondrial membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in phagocytic cup	IEA Inferred from Electronic Annotation more info
located_in phagocytic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: immunity-related GTPase family M protein

Names: LPS-stimulated RAW 264.7 macrophage protein 47 homolog; LRG-47-like protein; immunity-related GTPase family, M1; interferon-inducible protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_027809.2 RefSeqGene

Range

4999..7180

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001145805.2 → NP_001139277.1 immunity-related GTPase family M protein isoform 2

See identical proteins and their annotated locations for NP_001139277.1

Status: REVIEWED

Source sequence(s)

AC010441

Consensus CDS

CCDS47313.1

UniProtKB/Swiss-Prot

A1A4Y4, B3VEX0, H0YBM2

Related

ENSP00000428220.1, ENST00000522154.2

Conserved Domains (1) summary

cl21455
Location:33 → 180

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_001346557.2 → NP_001333486.1 immunity-related GTPase family M protein isoform 1

Status: REVIEWED

Source sequence(s)

AC010441

Conserved Domains (1) summary

cl38936
Location:33 → 179

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases