IRF2
interferon regulatory factor 2, the group of Interferon regulatory factors
Basic information
Region (hg38): 4:184385702-184474558
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRF2 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 2 |
Variants in IRF2
This is a list of pathogenic ClinVar variants found in the IRF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-184388826-G-A | not specified | Uncertain significance (May 02, 2024) | ||
| 4-184388828-T-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 4-184388861-G-A | not specified | Uncertain significance (Jul 06, 2021) | ||
| 4-184388899-G-A | Benign (Dec 31, 2019) | |||
| 4-184388913-C-G | not specified | Uncertain significance (May 17, 2023) | ||
| 4-184388967-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 4-184389018-T-A | not specified | Uncertain significance (Nov 30, 2022) | ||
| 4-184389039-T-G | not specified | Uncertain significance (Jul 05, 2022) | ||
| 4-184389051-G-A | not specified | Uncertain significance (Oct 13, 2023) | ||
| 4-184390739-C-T | Benign (Dec 31, 2019) | |||
| 4-184399021-C-T | not specified | Likely benign (Dec 14, 2023) | ||
| 4-184408164-T-A | not specified | Uncertain significance (Nov 30, 2022) | ||
| 4-184408172-G-A | not specified | Uncertain significance (Dec 17, 2023) | ||
| 4-184418533-T-C | not provided (-) | |||
| 4-184418696-G-C | not specified | Uncertain significance (Oct 12, 2021) | ||
| 4-184418697-G-A | not specified | Uncertain significance (Mar 20, 2024) | ||
| 4-184418697-G-C | not specified | Uncertain significance (May 02, 2024) | ||
| 4-184419566-TTC-T | Uncertain significance (Dec 18, 2017) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IRF2 | protein_coding | protein_coding | ENST00000393593 | 8 | 86868 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.798 | 0.202 | 125736 | 0 | 6 | 125742 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.31 | 122 | 218 | 0.560 | 0.0000133 | 2321 |
| Missense in Polyphen | 20 | 83.149 | 0.24053 | 833 | ||
| Synonymous | 0.676 | 76 | 83.9 | 0.906 | 0.00000568 | 645 |
| Loss of Function | 3.33 | 3 | 18.5 | 0.163 | 9.38e-7 | 198 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000386 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000386 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Specifically binds to the upstream regulatory region of type I IFN and IFN-inducible MHC class I genes (the interferon consensus sequence (ICS)) and represses those genes. Also acts as an activator for several genes including H4 and IL7. Constitutively binds to the ISRE promoter to activate IL7. Involved in cell cycle regulation through binding the site II (HiNF-M) promoter region of H4 and activating transcription during cell growth. Antagonizes IRF1 transcriptional activation. {ECO:0000269|PubMed:12738767, ECO:0000269|PubMed:15226432, ECO:0000269|PubMed:18514056, ECO:0000269|PubMed:9540062}.;
- Pathway
- Apoptosis;Apoptotic Signaling Pathway;Type II interferon signaling (IFNG);the information processing pathway at the ifn beta enhancer;Cytokine Signaling in Immune system;Factors involved in megakaryocyte development and platelet production;Immune System;Hemostasis;Interferon gamma signaling;Interferon alpha/beta signaling;Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- loftool
- 0.169
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 17.75
Haploinsufficiency Scores
- pHI
- 0.525
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.646
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.745
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Irf2
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; immune system phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;blood coagulation;cell population proliferation;positive regulation of transcription by RNA polymerase II;defense response to virus;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway
- Cellular component
- nucleoplasm;cytosol;focal adhesion
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding