U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

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

    Gene ID: 3664, updated on 4-Dec-2023

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See IRF6 in Genome Data Viewer
    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_000001.11Genomic 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

    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

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    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 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    interferon regulatory factor 6

    NCBI Reference Sequences (RefSeq)

    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_001206696.2NP_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
      B4DLE2, D3DT90, F5GWX8, G0ZTL0, O14896
      UniProtKB/TrEMBL
      B2R762, 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: GCF_000001405.40-RS_2023_10

    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)