IRGM
immunity related GTPase M
Basic information
Region (hg38): 5:150846521-150900736
Previous symbols: [ "IRGM1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (37 variants)
- not_provided (2 variants)
- IRGM-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRGM gene is commonly pathogenic or not. These statistics are base on transcript: NM_001145805.2. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 36 | 38 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IRGM | protein_coding | protein_coding | ENST00000522154 | 1 | 54214 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.414 | 84 | 95.4 | 0.881 | 0.00000447 | 1190 |
| Missense in Polyphen | 17 | 20.312 | 0.83695 | 294 | ||
| Synonymous | 0.132 | 34 | 35.0 | 0.972 | 0.00000156 | 361 |
| Loss of Function |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | ||
| East Asian | ||
| Finnish | ||
| European (Non-Finnish) | ||
| Middle Eastern | ||
| South Asian | ||
| Other |
dbNSFP
Source:
- Function
- FUNCTION: 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). {ECO:0000250, ECO:0000269|PubMed:16888103}.;
- Disease
- DISEASE: Inflammatory bowel disease 19 (IBD19) [MIM:612278]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. {ECO:0000269|PubMed:17554261, ECO:0000269|PubMed:19174780, ECO:0000269|PubMed:21278745}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Toxoplasmosis - Homo sapiens (human)
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.57
- rvis_percentile_EVS
- 81.78
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.165
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Irgm2
- Phenotype
Gene ontology
- Biological process
- autophagosome assembly;positive regulation of protein phosphorylation;defense response;inflammatory response;positive regulation of autophagy;positive regulation of peptidyl-threonine phosphorylation;protein destabilization;positive regulation of peptidyl-serine phosphorylation;cellular response to interferon-beta;defense response to bacterium;regulation of protein complex assembly;innate immune response;protein stabilization;defense response to Gram-negative bacterium;positive regulation of interferon-gamma-mediated signaling pathway;regulation of protein complex stability;protein lipidation involved in autophagosome assembly;CAMKK-AMPK signaling cascade;nucleotide-binding oligomerization domain containing 2 signaling pathway;cellular response to lipopolysaccharide;positive regulation of protein serine/threonine kinase activity;autophagy of host cells involved in interaction with symbiont;cellular response to virus;positive regulation of autophagosome maturation
- Cellular component
- Golgi membrane;autophagosome membrane;phagocytic cup;mitochondrion;endoplasmic reticulum membrane;Golgi apparatus;cytosol;phagocytic vesicle membrane;cell projection
- Molecular function
- GTPase activity;protein binding;GTP binding;protein kinase binding;protein serine/threonine kinase activator activity;CARD domain binding;BH3 domain binding