GeneBe

IRF2

protein-coding

interferon regulatory factor 2, the group of Interferon regulatory factors

Gene summary

IRF2 encodes interferon regulatory factor 2, a member of the interferon regulatory transcription factor (IRF) family. IRF2 competitively inhibits the IRF1-mediated transcriptional activation of interferons alpha and beta, and presumably other genes that employ IRF1 for transcription activation. However, IRF2 also functions as a transcriptional activator of histone H4. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002199.4

Inheritance

—

ClinVar variants

U:46B:5

Top phenotype

IRF2-related condition

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr4:184,385,702-184,474,558

External References & Databases

Ensembl (ENSG00000168310)NCBI Gene (3660)OMIM (147576)HGNC:6117GenCCUniProt (P14316)AlphaFoldClinVar (IRF2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~88.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IRF2 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 35
not providedTotal: 4
IRF2-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002199.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
clinvar
2
clinvar
 6
missense
38
clinvar
1
clinvar
 39
nonsense
1
clinvar
 1
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
4
clinvar
 4
Total00463251
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002199.4RefSeqNP_002190.28MANE Select
ENST00000393593.8EnsemblENSP00000377218.38MANE Select
ENST00000502750.2EnsemblENSP00000423074.26Standard
ENST00000502750.3EnsemblENSP00000423074.26Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Apoptosis
  • Apoptotic Signaling Pathway
  • Type II interferon signaling (IFNG)
  • the information processing pathway at the ifn beta enhancer
  • Cytokine Signaling in Immune system

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

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

Cellular Component

  • nucleoplasm
  • cytosol
  • focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000393593
Coding exons
8
Length
86868
Individuals with no LoFs
125736
Homozygous LoFs
0
Heterozygous LoFs
6
Defined
125742
p
0.0000239
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.311222180.5600.00001332321
Missense (PolyPhen)2083.1490.24053833
Synonymous0.6767683.90.9060.00000568645
Loss of Function3.33318.50.1639.38e-7198

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000390.000035rare
South Asian0.0000390.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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}.;

Recessive Scores

pRec
0.116

Intolerance Scores

LoFtool
0.169
RVIS EVS
-0.6
RVIS percentile EVS
17.75

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
K
Indispensability pred.
E
Indispensability score
0.745

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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