IRF6 interferon regulatory factor 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: IRF6provided by HGNC
Official Full Name: interferon regulatory factor 6provided by HGNC
Primary source: HGNC:HGNC:6121
See related: Ensembl:ENSG00000117595 MIM:607199; AllianceGenome:HGNC:6121
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LPS; PIT; PPS; VWS; OFC6; PPS1; VWS1
Summary: This gene encodes a member of the interferon regulatory transcription factor (IRF) family. Family members share a highly-conserved N-terminal helix-turn-helix DNA-binding domain and a less conserved C-terminal protein-binding domain. The encoded protein may be a transcriptional activator. Mutations in this gene can cause van der Woude syndrome and popliteal pterygium syndrome. Mutations in this gene are also associated with non-syndromic orofacial cleft type 6. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2011]
Expression: Broad expression in skin (RPKM 34.2), esophagus (RPKM 31.3) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q32.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (209785617..209806142, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (209032385..209052912, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (209958962..209979487, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Review on the Role of IRF6 in the Pathogenesis of Non-syndromic Orofacial Clefts.
Title: Review on the Role of IRF6 in the Pathogenesis of Non-syndromic Orofacial Clefts.
Identification and validation of IRF6 related to ovarian cancer and biological function and prognostic value.
Title: Identification and validation of IRF6 related to ovarian cancer and biological function and prognostic value.
Biophysical and functional characterization of N-terminal domain of Human Interferon Regulatory Factor 6.
Title: Biophysical and functional characterization of N-terminal domain of Human Interferon Regulatory Factor 6.
[Correlation between methylation of interferon regulatory factor 6 gene promoter in renal tissues and overall survival of patients with Kidney renal clear cell carcinoma].
Title: [Correlation between methylation of interferon regulatory factor 6 gene promoter in renal tissues and overall survival of patients with Kidney renal clear cell carcinoma].
Association between IRF6, TP63, GREM1 Gene Polymorphisms and Non-Syndromic Orofacial Cleft Phenotypes in Vietnamese Population: A Case-Control and Family-Based Study.
Title: Association between IRF6, TP63, GREM1 Gene Polymorphisms and Non-Syndromic Orofacial Cleft Phenotypes in Vietnamese Population: A Case-Control and Family-Based Study.
A Variant in the IRF6 Promoter Associated with the Risk for Orofacial Clefting.
Title: A Variant in the IRF6 Promoter Associated with the Risk for Orofacial Clefting.
A Complex Intrachromosomal Rearrangement Disrupting IRF6 in a Family with Popliteal Pterygium and Van der Woude Syndromes.
Title: A Complex Intrachromosomal Rearrangement Disrupting IRF6 in a Family with Popliteal Pterygium and Van der Woude Syndromes.
Association between variants around IRF6 and non-syndromic orofacial cleft in Western Han Chinese.
Title: Association between variants around IRF6 and non-syndromic orofacial cleft in Western Han Chinese.
A Comprehensive Genetic Analysis of Slovenian Families with Multiple Cases of Orofacial Clefts Reveals Novel Variants in the Genes IRF6, GRHL3, and TBX22.
Title: A Comprehensive Genetic Analysis of Slovenian Families with Multiple Cases of Orofacial Clefts Reveals Novel Variants in the Genes IRF6, GRHL3, and TBX22.
The IRF6 AP-2alpha binding site polymorphism relate to the severity of non-syndromic orofacial cleft of Indonesian patients.
Title: The IRF6 AP-2α binding site polymorphism relate to the severity of non-syndromic orofacial cleft of Indonesian patients.

Submit: New GeneRIF Correction See all GeneRIFs (167)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal dominant popliteal pterygium syndrome MedGen: CN296406 OMIM: 119500 GeneReviews: IRF6-Related Disorders	Compare labs
Orofacial cleft 6, susceptibility to MedGen: C1837213 OMIM: 608864 GeneReviews: Not available	Compare labs
Van der Woude syndrome 1 MedGen: C4551864 OMIM: 119300 GeneReviews: IRF6-Related Disorders	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2012-07-06) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2012-07-06) ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-76222 (e-PCR)
- UniSTS:58632

MARC_24336-24337:1030113089:1 (e-PCR)
- UniSTS:268888

D1S3693 (e-PCR)
- UniSTS:474271

RH67815 (e-PCR)
- UniSTS:92086

RH98921 (e-PCR)
- UniSTS:88317

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell development	IEA Inferred from Electronic Annotation more info
involved_in cranial skeletal system development	IEA Inferred from Electronic Annotation more info
involved_in immune system process	IBA Inferred from Biological aspect of Ancestor more info
involved_in keratinocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in limb development	IEA Inferred from Electronic Annotation more info
involved_in mammary gland epithelial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of stem cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in roof of mouth development	IEA Inferred from Electronic Annotation more info
involved_in stem cell proliferation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: interferon regulatory factor 6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007081.2 RefSeqGene

Range

4993..25518

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001206696.2 → NP_001193625.1 interferon regulatory factor 6 isoform 2

See identical proteins and their annotated locations for NP_001193625.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK296960, AL022398, DA016081

Consensus CDS

CCDS55681.1

UniProtKB/Swiss-Prot

O14896

Related

ENSP00000440532.1, ENST00000542854.5

Conserved Domains (1) summary

pfam10401
Location:129 → 312

IRF-3; Interferon-regulatory factor 3
NM_006147.4 → NP_006138.1 interferon regulatory factor 6 isoform 1

See identical proteins and their annotated locations for NP_006138.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL022398, BC014852, DA016081

Consensus CDS

CCDS1492.1

UniProtKB/Swiss-Prot

B4DLE2, D3DT90, F5GWX8, G0ZTL0, O14896

UniProtKB/TrEMBL

B2R762, G0Z349

Related

ENSP00000355988.3, ENST00000367021.8

Conserved Domains (2) summary

pfam00605
Location:9 → 114

IRF; Interferon regulatory factor transcription factor

pfam10401
Location:224 → 407

IRF-3; Interferon-regulatory factor 3