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

Gene ID: 345611, updated on 17-Jun-2019

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
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; 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

Genomic context

See IRGM in Genome Data Viewer
Location:
5q33.1
Exon count:
4
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (150846521..150902402)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (150226085..150228231)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene dynactin subunit 4 Neighboring gene small integral membrane protein 3 Neighboring gene zinc finger protein 300 Neighboring gene zinc finger protein 300 pseudogene 1 Neighboring gene zinc finger protein 35 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

NHGRI GWAS Catalog

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

HIV-1 interactions

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

Pathways from BioSystems

  • Toxoplasmosis, organism-specific biosystem (from KEGG)
    Toxoplasmosis, organism-specific biosystemToxoplasma gondii is an obligate intracellular parasite that is prevalent worldwide. The tachyzoite form acquired by oral ingestion downmodulates proinflammatory signaling pathways via various mechan...
  • Toxoplasmosis, conserved biosystem (from KEGG)
    Toxoplasmosis, conserved biosystemToxoplasma gondii is an obligate intracellular parasite that is prevalent worldwide. The tachyzoite form acquired by oral ingestion downmodulates proinflammatory signaling pathways via various mechan...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC149263, MGC149264

Gene Ontology Provided by GOA

Function Evidence Code Pubs
BH3 domain binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
CARD domain binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
GTP binding IEA
Inferred from Electronic Annotation
more info
 
GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein serine/threonine kinase activator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
CAMKK-AMPK signaling cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
autophagy of host cells involved in interaction with symbiont IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to interferon-beta IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to virus IMP
Inferred from Mutant Phenotype
more info
PubMed 
defense response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
defense response to Gram-negative bacterium IMP
Inferred from Mutant Phenotype
more info
PubMed 
defense response to bacterium IMP
Inferred from Mutant Phenotype
more info
PubMed 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleotide-binding oligomerization domain containing 2 signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interferon-gamma-mediated signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of peptidyl-serine phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of peptidyl-threonine phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein serine/threonine kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein destabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein lipidation involved in autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein complex stability IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane IDA
Inferred from Direct Assay
more info
PubMed 
autophagosome membrane IEA
Inferred from Electronic Annotation
more info
 
cell projection IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
phagocytic cup IEA
Inferred from Electronic Annotation
more info
 
phagocytic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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

  1. NG_027809.2 RefSeqGene

    Range
    5001..7147
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145805.1NP_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
    Related
    ENSP00000428220.1, ENST00000522154.1
    Conserved Domains (1) summary
    cl21455
    Location:33180
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  2. NM_001346557.2NP_001333486.1  immunity-related GTPase family M protein isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC010441

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    150846521..150902402
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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