IRF5

interferon regulatory factor 5, the group of Interferon regulatory factors

Basic information

Region (hg38): 7:128937457-128950038

Links

ENSG00000128604 ∙ NCBI:3663 ∙ OMIM:607218 ∙ HGNC:6120 ∙ Uniprot:Q13568 ∙ 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 IRF5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRF5 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				4	2	6
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	1	2
Total	0	0	30	6	4

Variants in IRF5

This is a list of pathogenic ClinVar variants found in the IRF5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-128937860-C-CGCGGG		Inflammatory bowel disease 14, susceptibility to • Systemic lupus erythematosus, susceptibility to, 10	risk factor (Mar 15, 2008)
7-128938247-T-T		Systemic lupus erythematosus, susceptibility to, 10 • Rheumatoid arthritis	Pathogenic; risk factor (Mar 15, 2008)
7-128939612-G-A			Benign (Feb 18, 2020)
7-128942097-C-G		not specified	Uncertain significance (Nov 09, 2022)
7-128942125-T-G		not specified	Uncertain significance (Nov 05, 2021)
7-128942286-G-A		IRF5-related disorder	Likely benign (Mar 22, 2019)
7-128945875-G-A		not specified	Uncertain significance (Jun 07, 2023)
7-128945898-G-A			Benign (May 21, 2018)
7-128945952-C-T			Likely benign (Jun 22, 2018)
7-128946003-C-T			Likely benign (Aug 02, 2018)
7-128946528-T-A		not specified	Uncertain significance (Sep 25, 2023)
7-128946536-G-A		not specified	Uncertain significance (Nov 22, 2022)
7-128946562-G-A			Benign (Dec 31, 2019)
7-128947242-C-T		not specified	Uncertain significance (Apr 04, 2023)
7-128947283-G-A		not specified	Uncertain significance (Jan 29, 2024)
7-128947289-T-A		not specified	Uncertain significance (Jun 11, 2021)
7-128947297-CACTCTGCAGCCGCCCACTCTGCGGCCGCCT-C			Benign (Dec 31, 2019)
7-128947323-C-T		not specified	Uncertain significance (Nov 20, 2023)
7-128947324-G-A			Benign (Dec 31, 2019)
7-128947353-C-T		not specified	Uncertain significance (Jul 15, 2021)
7-128947371-C-T		not specified	Uncertain significance (Jul 30, 2023)
7-128947398-C-A		not specified	Uncertain significance (Jun 13, 2023)
7-128947398-C-T		not specified	Uncertain significance (Apr 28, 2023)
7-128947464-T-C		not specified	Uncertain significance (Dec 16, 2023)
7-128947470-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRF5	protein_coding	protein_coding	ENST00000357234	8	12424

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00904	0.991	125706	0	41	125747	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	214	309	0.693	0.0000189	3314
Missense in Polyphen		72	150.44	0.47861		1588
Synonymous	0.552	116	124	0.937	0.00000712	1052
Loss of Function	3.06	8	24.3	0.330	0.00000129	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.000734
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000210	0.000167
Middle Eastern	0.0000546	0.0000544
South Asian	0.000205	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor involved in the induction of interferons IFNA and INFB and inflammatory cytokines upon virus infection. Activated by TLR7 or TLR8 signaling. {ECO:0000269|PubMed:11303025, ECO:0000269|PubMed:15695821}.
• Disease: DISEASE: Inflammatory bowel disease 14 (IBD14) [MIM:612245]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. {ECO:0000269|PubMed:17881657}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Systemic lupus erythematosus 10 (SLEB10) [MIM:612251]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269|PubMed:15657875}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Rheumatoid arthritis (RA) [MIM:180300]: An inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures. {ECO:0000269|PubMed:17599733}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Toll-like receptor signaling pathway - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Apoptosis;Vitamin D Receptor Pathway;Apoptotic Signaling Pathway;Senescence and Autophagy in Cancer;Toll-like Receptor Signaling Pathway;the information processing pathway at the ifn beta enhancer;Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Direct p53 effectors;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.0642
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.736
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Irf5
• Phenotype: immune system phenotype; hematopoietic system phenotype; normal phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to peptidoglycan;response to muramyl dipeptide;positive regulation of interferon-alpha production;positive regulation of interferon-beta production;positive regulation of interleukin-12 production;positive regulation of apoptotic process;positive regulation of transcription by RNA polymerase II;defense response to virus;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;identical protein binding;sequence-specific DNA binding;transcription regulatory region DNA binding