IFNGR2
interferon gamma receptor 2, the group of Fibronectin type III domain containing|Interferon receptors
Basic information
Region (hg38): 21:33403413-33479348
Previous symbols: [ "IFNGT1" ]
Links
Phenotypes
GenCC
Source:
- autosomal recessive Mendelian susceptibility to mycobacterial diseases due to complete IFNgammaR2 deficiency (Supportive), mode of inheritance: AR
- autosomal recessive Mendelian susceptibility to mycobacterial diseases due to partial IFNgammaR2 deficiency (Supportive), mode of inheritance: AR
- autosomal dominant mendelian susceptibility to mycobacterial diseases due to partial IFNgammaR2 deficiency (Supportive), mode of inheritance: AD
- immunodeficiency 28 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Immunodeficiency 28 | AR | Allergy/Immunology/Infectious | Individuals may be susceptible to frequent and severe mycobacterial infections, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial | Allergy/Immunology/Infectious | 15924140; 23161749; 31222290 |
ClinVar
This is a list of variants' phenotypes submitted to
- Immunodeficiency_28 (207 variants)
- not_provided (46 variants)
- Inborn_genetic_diseases (32 variants)
- IFNGR2-related_disorder (6 variants)
- not_specified (4 variants)
- Immunodeficiency_27A (2 variants)
- Susceptibility_to_severe_COVID-19 (1 variants)
- Interferon_gamma_receptor_deficiency (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNGR2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005534.4. 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 | 56 | 61 | ||||
| missense | 86 | 10 | 99 | |||
| nonsense | 1 | |||||
| start loss | 2 | 2 | ||||
| frameshift | 5 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 5 | 3 | 89 | 66 | 6 |
Highest pathogenic variant AF is 0.000006065799
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IFNGR2 | protein_coding | protein_coding | ENST00000290219 | 7 | 76454 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.953 | 0.0472 | 125724 | 0 | 3 | 125727 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.828 | 138 | 168 | 0.820 | 0.00000983 | 2167 |
| Missense in Polyphen | 33 | 50.461 | 0.65397 | 679 | ||
| Synonymous | 0.210 | 67 | 69.2 | 0.968 | 0.00000484 | 672 |
| Loss of Function | 3.22 | 1 | 14.0 | 0.0714 | 6.79e-7 | 168 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Associates with IFNGR1 to form a receptor for the cytokine interferon gamma (IFNG) (PubMed:8124716, PubMed:7673114,PubMed:7615558). Ligand binding stimulates activation of the JAK/STAT signaling pathway (PubMed:8124716, PubMed:7673114, PubMed:15356148). Required for signal transduction in contrast to other receptor subunit responsible for ligand binding (PubMed:7673114). {ECO:0000269|PubMed:15356148, ECO:0000269|PubMed:7615558, ECO:0000269|PubMed:7673114, ECO:0000269|PubMed:8124716}.;
- Pathway
- Salmonella infection - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Influenza A - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Necroptosis - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);JAK-STAT-Core;The human immune response to tuberculosis;Type II interferon signaling (IFNG);Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Regulation of IFNG signaling;Immune System;IFN gamma signaling;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;Interferon gamma signaling;Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.163
Intolerance Scores
- loftool
- rvis_EVS
- 0.66
- rvis_percentile_EVS
- 84.55
Haploinsufficiency Scores
- pHI
- 0.103
- hipred
- Y
- hipred_score
- 0.546
- ghis
- 0.532
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.883
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ifngr2
- Phenotype
- hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- cell surface receptor signaling pathway;response to virus;cytokine-mediated signaling pathway;interferon-gamma-mediated signaling pathway;regulation of interferon-gamma-mediated signaling pathway
- Cellular component
- Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;cytoplasmic vesicle membrane
- Molecular function
- cytokine receptor activity;interferon-gamma receptor activity