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

    Gene ID: 3664, updated on 10-Dec-2024

    Summary

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    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

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    See IRF6 in Genome Data Viewer
    Location:
    1q32.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (209785617..209806142, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (209032385..209052912, complement)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 2470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2473 Neighboring gene adenosine A2b receptor pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:209944889-209945388 Neighboring gene MPRA-validated peak675 silencer Neighboring gene TRAF3 interacting protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:209957609-209958226 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:209958227-209958842 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:209979409-209979752 Neighboring gene chromosome 1 open reading frame 74 Neighboring gene VISTA enhancer hs932 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2477 Neighboring gene Sharpr-MPRA regulatory region 1786 Neighboring gene UTP25 small subunit processome component Neighboring gene NANOG hESC enhancer GRCh37_chr1:210048900-210049401 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:210068740-210069939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:210071837-210072364 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2736 Neighboring gene Sharpr-MPRA regulatory region 13960 Neighboring gene synaptotagmin 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:210166703-210167203 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2861 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2872 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2922 Neighboring gene NANOG hESC enhancer GRCh37_chr1:210284477-210284996 Neighboring gene MPRA-validated peak677 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_2948

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. IRF6 polymorphisms are associated with nonsyndromic orofacial clefts in a Chinese Han population. Pan Y, et al. Am J Med Genet A, 2010 Oct. PMID 20799332
    2. Contribution of variants in and near the IRF6 gene to the risk of nonsyndromic cleft lip with or without cleft palate in a Malay population. Salahshourifar I, et al. Am J Med Genet A, 2011 Sep. PMID 21834040
    3. Association of common variants, not rare mutations, in IRF6 with nonsyndromic clefts in a Honduran population. Larrabee YC, et al. Laryngoscope, 2011 Aug. PMID 21792966
    4. Monozygotic twins with variable expression of Van der Woude syndrome. Jobling R, et al. Am J Med Genet A, 2011 Aug. PMID 21739575, Free PMC Article
    5. Novel IRF6 mutations in Honduran Van der Woude syndrome patients. Birkeland AC, et al. Mol Med Rep, 2011 Mar-Apr. PMID 21468557

    See all (200) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel noncanonical function for IRF6 in the recycling of E-cadherin.
      Title: A novel noncanonical function for IRF6 in the recycling of E-cadherin.
    2. Causal Variations at IRF6 Gene Identified in Van der Woude Syndrome Pedigrees.
      Title: Causal Variations at IRF6 Gene Identified in Van der Woude Syndrome Pedigrees.
    3. 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.
    4. 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.
    5. 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.
    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].
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (169)

    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

    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
    Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
    EBI GWAS Catalog
    Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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
    located_in 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 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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    NEW Try the new Transcript table

    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_001206696.2 → 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

    2. 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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      209032385..209052912 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14896.1 GenPept UniProtKB/Swiss-Prot:O14896

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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