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

Gene ID: 3664, updated on 3-Jan-2016
Official Symbol
IRF6provided by HGNC
Official Full Name
interferon regulatory factor 6provided by HGNC
Primary source
HGNC:HGNC:6121
See related
Ensembl:ENSG00000117595; HPRD:06227; MIM:607199; Vega:OTTHUMG00000036521
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]
Orthologs
See IRF6 in Epigenomics, MapViewer
Location:
1q32.3-q41
Exon count:
9
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 1 NC_000001.11 (209785623..209806175, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (209958968..209979520, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101930114 Neighboring gene adenosine A2b receptor pseudogene 1 Neighboring gene TRAF3 interacting protein 3 Neighboring gene chromosome 1 open reading frame 74 Neighboring gene digestive organ expansion factor homolog (zebrafish) Neighboring gene synaptotagmin 14

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Orofacial cleft 6, susceptibility to
MedGen: C1837213 OMIM: 608864 GeneReviews: Not available
Compare labs
Popliteal pterygium syndrome
MedGen: C0265259 OMIM: 119500 GeneReviews: IRF6-Related Disorders
Compare labs
Van der Woude syndrome
MedGen: C0175697 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

NHGRI GWAS Catalog

Description
A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4.
NHGRI GWA Catalog
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
NHGRI GWA Catalog
Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24.
NHGRI GWA Catalog
  • Apoptosis, organism-specific biosystem (from WikiPathways)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Interferon Signaling, organism-specific biosystem (from REACTOME)
    Interferon Signaling, organism-specific biosystemInterferons (IFNs) are cytokines that play a central role in initiating immune responses, especially antiviral and antitumor effects. There are three types of IFNs:Type I (IFN-alpha, -beta and others...
  • Interferon alpha/beta signaling, organism-specific biosystem (from REACTOME)
    Interferon alpha/beta signaling, organism-specific biosystemType I interferons (IFNs) are composed of various genes including IFN alpha (IFNA), beta (IFNB), omega, epsilon, and kappa. In humans the IFNA genes are composed of more than 13 subfamily genes, wher...
  • Interferon gamma signaling, organism-specific biosystem (from REACTOME)
    Interferon gamma signaling, organism-specific biosystemInterferon-gamma (IFN-gamma) belongs to the type II interferon family and is secreted by activated immune cells-primarily T and NK cells, but also B-cells and APC. INFG exerts its effect on cells by ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
regulatory region DNA binding IEA
Inferred from Electronic Annotation
more info
 
transcription factor activity, sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
cell cycle arrest IDA
Inferred from Direct Assay
more info
PubMed 
cell development IEA
Inferred from Electronic Annotation
more info
 
cytokine-mediated signaling pathway TAS
Traceable Author Statement
more info
 
interferon-gamma-mediated signaling pathway TAS
Traceable Author Statement
more info
 
keratinocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
keratinocyte proliferation IEA
Inferred from Electronic Annotation
more info
 
mammary gland epithelial cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
type I interferon signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
interferon regulatory factor 6

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
    4960..25512
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206696.1NP_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, ENST00000542854
    Conserved Domains (1) summary
    pfam10401
    Location:128312
    IRF-3; Interferon-regulatory factor 3
  2. NM_006147.3NP_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/TrEMBL
    G0Z349
    UniProtKB/Swiss-Prot
    O14896
    Related
    ENSP00000355988, OTTHUMP00000034677, ENST00000367021, OTTHUMT00000088827
    Conserved Domains (2) summary
    cd00103
    Location:7115
    IRF; Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The ...
    pfam10401
    Location:223407
    IRF-3; Interferon-regulatory factor 3

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p2 Primary Assembly

    Range
    209785623..209806175 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 Alternate CHM1_1.1

    Range
    211231296..211251831 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)