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

Gene ID: 3664, updated on 17-Oct-2021

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
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
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Genomic context

See IRF6 in Genome Data Viewer
Location:
1q32.2
Exon count:
9
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (209785617..209806142, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (209958962..209979487, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene adenosine A2b receptor pseudogene 1 Neighboring gene TRAF3 interacting protein 3 Neighboring gene chromosome 1 open reading frame 74 Neighboring gene VISTA enhancer hs932 Neighboring gene UTP25 small subunit processor component Neighboring gene Sharpr-MPRA regulatory region 1786

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4.
GeneReviews: Not available
Autosomal dominant popliteal pterygium syndrome
MedGen: CN296406 OMIM: 119500 GeneReviews: IRF6-Related Disorders
not available
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
GeneReviews: Not available
Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24.
GeneReviews: Not available
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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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
PubMed 
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 positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of cell cycle 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
PubMed 
involved_in roof of mouth development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cell junction IDA
Inferred from Direct Assay
more info
 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in extracellular exosome HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

  1. NG_007081.2 RefSeqGene

    Range
    4993..25518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206696.2NP_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:129312
    IRF-3; Interferon-regulatory factor 3
  2. NM_006147.4NP_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
    O14896
    UniProtKB/TrEMBL
    G0Z349
    Related
    ENSP00000355988.3, ENST00000367021.8
    Conserved Domains (2) summary
    pfam00605
    Location:9114
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:224407
    IRF-3; Interferon-regulatory factor 3

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    209785617..209806142 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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