IRF2

interferon regulatory factor 2, the group of Interferon regulatory factors

Basic information

Region (hg38): 4:184385701-184474558

Links

ENSG00000168310 ∙ NCBI:3660 ∙ OMIM:147576 ∙ HGNC:6117 ∙ Uniprot:P14316 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IRF2 gene.

• Inborn genetic diseases (7 variants)
• not provided (3 variants)

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					2	2
missense			7			7
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	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
4-184388828-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)
4-184418696-G-C		not specified	Uncertain significance (Oct 12, 2021)
4-184419566-TTC-T			Uncertain significance (Dec 18, 2017)

GnomAD

Source: gnomAD

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: 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}.
• 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