IRF2BP1

interferon regulatory factor 2 binding protein 1

Basic information

Region (hg38): 19:45883608-45886141

Links

ENSG00000170604 ∙ NCBI:26145 ∙ OMIM:615331 ∙ HGNC:21728 ∙ Uniprot:Q8IU81 ∙ 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 IRF2BP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRF2BP1 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	2

Variants in IRF2BP1

This is a list of pathogenic ClinVar variants found in the IRF2BP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-45884086-G-A			Benign (Nov 02, 2021)
19-45884112-C-T		not specified	Uncertain significance (Jul 05, 2023)
19-45884151-C-T		not specified	Uncertain significance (Jun 28, 2024)
19-45884165-G-T		not specified	Uncertain significance (Nov 06, 2023)
19-45884168-T-C		not specified	Uncertain significance (Jan 19, 2025)
19-45884245-T-C			Benign (Nov 02, 2021)
19-45884280-C-G		not specified	Uncertain significance (Nov 10, 2024)
19-45884328-C-T		not specified	Uncertain significance (Dec 14, 2024)
19-45884396-G-A		not specified	Uncertain significance (May 30, 2024)
19-45884439-G-C		not specified	Uncertain significance (Jun 16, 2023)
19-45884457-G-C		not specified	Uncertain significance (Jul 16, 2024)
19-45884513-G-C		not specified	Uncertain significance (Nov 08, 2022)
19-45884567-C-T		not specified	Uncertain significance (Feb 20, 2025)
19-45884576-T-C		not specified	Uncertain significance (May 11, 2022)
19-45884582-T-G		not specified	Uncertain significance (Apr 20, 2023)
19-45884628-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-45884636-C-T		not specified	Uncertain significance (Feb 25, 2025)
19-45884645-G-A		not specified	Uncertain significance (Nov 11, 2024)
19-45884651-G-T		not specified	Uncertain significance (Nov 09, 2023)
19-45884661-G-A		not specified	Uncertain significance (Dec 27, 2022)
19-45884690-A-G		not specified	Uncertain significance (Mar 18, 2024)
19-45884697-C-G		not specified	Uncertain significance (Mar 25, 2024)
19-45884834-T-C		not specified	Uncertain significance (May 08, 2024)
19-45884991-T-C		not specified	Likely benign (Jul 20, 2022)
19-45885104-C-T		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRF2BP1	protein_coding	protein_coding	ENST00000302165	1	2511

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00976	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.34	198	382	0.519	0.0000265	3621
Missense in Polyphen		25	77.476	0.32268		727
Synonymous	0.823	167	181	0.922	0.0000136	1322
Loss of Function	3.75	1	18.3	0.0546	0.00000114	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional corepressor in a IRF2- dependent manner; this repression is not mediated by histone deacetylase activities. May act as an E3 ligase towards JDP2, enhancing its polyubiquitination. Represses ATF2-dependent transcriptional activation. {ECO:0000269|PubMed:12799427, ECO:0000269|PubMed:18671972}.
• Pathway: TGF_beta_Receptor (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.0271
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.546
• hipred: Y
• hipred_score: 0.717
• ghis: 0.477

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Irf2bp1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;transferase activity;metal ion binding