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Aliases for IRF6 Gene

Aliases for IRF6 Gene

  • Interferon Regulatory Factor 6 2 3 5
  • Van Der Woude Syndrome 2
  • IRF-6 4
  • VWS1 3
  • OFC6 3
  • PPS1 3
  • PPS 3
  • PIT 3
  • LPS 3
  • VWS 3

External Ids for IRF6 Gene

Previous HGNC Symbols for IRF6 Gene

  • VWS
  • LPS

Previous GeneCards Identifiers for IRF6 Gene

  • GC01M208600
  • GC01M205667
  • GC01M206600
  • GC01M207040
  • GC01M206349
  • GC01M208025
  • GC01M209959
  • GC01M180637

Summaries for IRF6 Gene

Entrez Gene Summary for IRF6 Gene

  • 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]

GeneCards Summary for IRF6 Gene

IRF6 (Interferon Regulatory Factor 6) is a Protein Coding gene. Diseases associated with IRF6 include Van Der Woude Syndrome and Popliteal Pterygium Syndrome 1. Among its related pathways are Interferon gamma signaling and Innate Immune System. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and regulatory region DNA binding. An important paralog of this gene is IRF5.

UniProtKB/Swiss-Prot for IRF6 Gene

  • Probable DNA-binding transcriptional activator. Key determinant of the keratinocyte proliferation-differentiation switch involved in appropriate epidermal development (By similarity). Plays a role in regulating mammary epithelial cell proliferation (By similarity). May regulate WDR65 transcription (By similarity).

Gene Wiki entry for IRF6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IRF6 Gene

Genomics for IRF6 Gene

Regulatory Elements for IRF6 Gene

Enhancers for IRF6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G209800 1.8 FANTOM5 Ensembl ENCODE dbSUPER 28.5 +0.3 255 10.2 HDGF PKNOX1 CREB3L1 ARNT SIN3A FEZF1 ZNF2 YY1 FOS ZNF263 IRF6 TRAF3IP3 DIEXF SYT14 LAMB3 C1orf74
GH01G209822 1.6 Ensembl ENCODE dbSUPER 21.1 -19.5 -19518 6.3 HDGF PKNOX1 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 IRF6 DIEXF SYT14 C1orf74 LOC101930114 TRAF3IP3
GH01G209814 1.8 VISTA FANTOM5 ENCODE dbSUPER 17.6 -9.9 -9923 3.9 SOX5 GATAD2A CTCF ZNF654 ZSCAN4 MNT REST ZNF501 EBF1 RAD21 IRF6 C1orf74 LOC101930114 SYT14 LAMB3 DIEXF
GH01G209782 1.4 ENCODE dbSUPER 20.7 +20.5 20528 6.0 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A ZNF2 YY1 ZNF766 CBX5 IRF6 TRAF3IP3 SYT14 C1orf74
GH01G209838 1.3 Ensembl ENCODE dbSUPER 20.6 -34.0 -33964 4.1 SIN3A RAD21 YY1 GATA2 SCRT2 RCOR1 FOS ELK4 CEBPB NR2F2 IRF6 SYT14 TRAF3IP3 DIEXF GC01M209934
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around IRF6 on UCSC Golden Path with GeneCards custom track

Promoters for IRF6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000019422 275 1001 HDGF PKNOX1 ATF1 CREB3L1 ARNT ZNF2 ELK1 SP3 CREB3 SMARCA4

Genomic Location for IRF6 Gene

Chromosome:
1
Start:
209,785,623 bp from pter
End:
209,806,175 bp from pter
Size:
20,553 bases
Orientation:
Minus strand

Genomic View for IRF6 Gene

Genes around IRF6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IRF6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IRF6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IRF6 Gene

Proteins for IRF6 Gene

  • Protein details for IRF6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14896-IRF6_HUMAN
    Recommended name:
    Interferon regulatory factor 6
    Protein Accession:
    O14896
    Secondary Accessions:
    • B4DLE2
    • D3DT90
    • F5GWX8
    • G0ZTL0

    Protein attributes for IRF6 Gene

    Size:
    467 amino acids
    Molecular mass:
    53130 Da
    Quaternary structure:
    • Interacts with SERPINB5.

    Alternative splice isoforms for IRF6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for IRF6 Gene

Post-translational modifications for IRF6 Gene

  • Phosphorylated. Phosphorylation status depends on the cell cycle and is a signal for ubiquitination and proteasome-mediated degradation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for IRF6 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for IRF6 (IRF6)
  • Santa Cruz Biotechnology (SCBT) Antibodies for IRF6

No data available for DME Specific Peptides for IRF6 Gene

Domains & Families for IRF6 Gene

Suggested Antigen Peptide Sequences for IRF6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O14896

UniProtKB/Swiss-Prot:

IRF6_HUMAN :
  • Belongs to the IRF family.
Family:
  • Belongs to the IRF family.
genes like me logo Genes that share domains with IRF6: view

No data available for Gene Families for IRF6 Gene

Function for IRF6 Gene

Molecular function for IRF6 Gene

GENATLAS Biochemistry:
interferon regulatory factor 6
UniProtKB/Swiss-Prot Function:
Probable DNA-binding transcriptional activator. Key determinant of the keratinocyte proliferation-differentiation switch involved in appropriate epidermal development (By similarity). Plays a role in regulating mammary epithelial cell proliferation (By similarity). May regulate WDR65 transcription (By similarity).

Gene Ontology (GO) - Molecular Function for IRF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000975 regulatory region DNA binding IEA --
GO:0003677 DNA binding ISS --
GO:0003700 transcription factor activity, sequence-specific DNA binding ISS --
GO:0005515 protein binding IPI 16049006
genes like me logo Genes that share ontologies with IRF6: view
genes like me logo Genes that share phenotypes with IRF6: view

Human Phenotype Ontology for IRF6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for IRF6 Gene

MGI Knock Outs for IRF6:

Animal Model Products

miRNA for IRF6 Gene

miRTarBase miRNAs that target IRF6

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for IRF6 Gene

Localization for IRF6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IRF6 Gene

Nucleus. Cytoplasm. Note=Translocates to nucleus in response to an activating signal. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for IRF6 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
mitochondrion 3
plasma membrane 2
peroxisome 2
lysosome 1
endosome 1

Gene Ontology (GO) - Cellular Components for IRF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005737 cytoplasm IDA,IEA 16049006
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with IRF6: view

Pathways & Interactions for IRF6 Gene

genes like me logo Genes that share pathways with IRF6: view

Gene Ontology (GO) - Biological Process for IRF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007050 cell cycle arrest IDA 18212048
GO:0008285 negative regulation of cell proliferation IDA 18212048
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with IRF6: view

No data available for SIGNOR curated interactions for IRF6 Gene

Transcripts for IRF6 Gene

Unigene Clusters for IRF6 Gene

Interferon regulatory factor 6:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for IRF6 Gene

No ASD Table

Relevant External Links for IRF6 Gene

GeneLoc Exon Structure for
IRF6
ECgene alternative splicing isoforms for
IRF6

Expression for IRF6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for IRF6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for IRF6 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x7.7), Skin - Sun Exposed (Lower leg) (x7.4), and Esophagus - Mucosa (x6.3).

Protein differential expression in normal tissues from HIPED for IRF6 Gene

This gene is overexpressed in Adrenal (16.0), Salivary gland (12.5), and Tonsil (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for IRF6 Gene



Protein tissue co-expression partners for IRF6 Gene

NURSA nuclear receptor signaling pathways regulating expression of IRF6 Gene:

IRF6

SOURCE GeneReport for Unigene cluster for IRF6 Gene:

Hs.591415

mRNA Expression by UniProt/SwissProt for IRF6 Gene:

O14896-IRF6_HUMAN
Tissue specificity: Expressed in normal mammary epithelial cells. Expression is reduced or absent in breast carcinomas.

Evidence on tissue expression from TISSUES for IRF6 Gene

  • Intestine(2.8)
  • Nervous system(2.8)
  • Skin(2.7)
  • Blood(2.4)
  • Heart(2.4)
  • Liver(2.3)
  • Muscle(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for IRF6 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeleton
Organs:
Head and neck:
  • brain
  • chin
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • pharynx
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
  • testicle
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with IRF6: view

Primer Products

Orthologs for IRF6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for IRF6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia IRF6 34 35
  • 99.57 (n)
dog
(Canis familiaris)
Mammalia IRF6 34 35
  • 93.94 (n)
cow
(Bos Taurus)
Mammalia IRF6 34 35
  • 93.72 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia IRF6 35
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Irf6 34
  • 90.65 (n)
mouse
(Mus musculus)
Mammalia Irf6 34 16 35
  • 90.44 (n)
oppossum
(Monodelphis domestica)
Mammalia IRF6 35
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves IRF6 34 35
  • 78.36 (n)
lizard
(Anolis carolinensis)
Reptilia IRF6 35
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia irf6 34
  • 74.51 (n)
Str.6728 34
African clawed frog
(Xenopus laevis)
Amphibia xIRF-6 34
zebrafish
(Danio rerio)
Actinopterygii irf6 34 35
  • 69.38 (n)
zgc63500 34
Species where no ortholog for IRF6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for IRF6 Gene

ENSEMBL:
Gene Tree for IRF6 (if available)
TreeFam:
Gene Tree for IRF6 (if available)

Paralogs for IRF6 Gene

Paralogs for IRF6 Gene

(3) SIMAP similar genes for IRF6 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with IRF6: view

Variants for IRF6 Gene

Sequence variations from dbSNP and Humsavar for IRF6 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs121434226 Pathogenic, Popliteal pterygium syndrome (PPS) [MIM:119500] 209,796,477(-) AGCTG(C/T)GCTGT reference, missense, utr-variant-5-prime
rs121434227 Pathogenic, Popliteal pterygium syndrome (PPS) [MIM:119500], Popliteal pterygium syndrome (PPS) [MIM:119500] 209,796,476(-) GCTGC(A/G/T)CTGTG reference, missense, utr-variant-5-prime
rs121434229 Pathogenic, Van der Woude syndrome 1 (VWS1) [MIM:119300] 209,801,280(-) CACCC(A/G)GCATA intron-variant, reference, missense
rs121434230 Pathogenic, Van der Woude syndrome 1 (VWS1) [MIM:119300] 209,788,638(-) TCATT(C/T)CAGTA reference, missense
rs121434231 Pathogenic, Van der Woude syndrome 1 (VWS1) [MIM:119300] 209,790,539(-) TGAGA(G/T)ACAAA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for IRF6 Gene

Variant ID Type Subtype PubMed ID
dgv144e212 CNV loss 25503493
nsv1006632 CNV gain 25217958
nsv4343 CNV deletion 18451855
nsv945273 CNV duplication 23825009

Variation tolerance for IRF6 Gene

Residual Variation Intolerance Score: 27.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.82; 79.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for IRF6 Gene

Human Gene Mutation Database (HGMD)
IRF6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
IRF6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IRF6 Gene

Disorders for IRF6 Gene

MalaCards: The human disease database

(21) MalaCards diseases for IRF6 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
van der woude syndrome
  • myopathy, actin, congenital, with excess of thin myofilaments
popliteal pterygium syndrome 1
  • popliteal pterygium syndrome
orofacial cleft 6
  • orofacial cleft 6, susceptibility to
tooth agenesis
  • familial tooth agenesis
irf6-related disorders
- elite association - COSMIC cancer census association via MalaCards
Search IRF6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

IRF6_HUMAN
  • Non-syndromic orofacial cleft 6 (OFC6) [MIM:608864]: A birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. {ECO:0000269 PubMed:15317890, ECO:0000269 PubMed:21082654}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Popliteal pterygium syndrome (PPS) [MIM:119500]: An autosomal dominant disorder characterized by oro-facial, skin and genital anomalies. Expressivity is variable. Clinical features include cleft lip/palate, lower lip cysts, syngnathia, congenital ankyloblepharon filiforme in some cases, bifid scrotum, hypoplastic scrotum, hypoplastic uterus, talipes equinovarus. {ECO:0000269 PubMed:12219090, ECO:0000269 PubMed:14640121, ECO:0000269 PubMed:19036739, ECO:0000269 PubMed:20803643}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Van der Woude syndrome 1 (VWS1) [MIM:119300]: An autosomal dominant developmental disorder characterized by lower lip pits, cleft lip and/or cleft palate. {ECO:0000269 PubMed:12219090, ECO:0000269 PubMed:12920575, ECO:0000269 PubMed:14618417, ECO:0000269 PubMed:14640121, ECO:0000269 PubMed:15300989, ECO:0000269 PubMed:17122170, ECO:0000269 PubMed:18478600, ECO:0000269 PubMed:19036739}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for IRF6

Genetic Association Database (GAD)
IRF6
Human Genome Epidemiology (HuGE) Navigator
IRF6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
IRF6
genes like me logo Genes that share disorders with IRF6: view

No data available for Genatlas for IRF6 Gene

Publications for IRF6 Gene

  1. Mutations in IRF6 cause Van der Woude and popliteal pterygium syndromes. (PMID: 12219090) Kondo S. … Murray J.C. (Nat. Genet. 2002) 2 3 4 22 64
  2. Lack of association between IRF6 polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian population. (PMID: 19780991) ParanaA-ba L.M. … Coletta R.D. (Oral Dis 2010) 3 22 46 64
  3. Missense mutations that cause Van der Woude syndrome and popliteal pterygium syndrome affect the DNA-binding and transcriptional activation functions of IRF6. (PMID: 19036739) Little H.J. … Shore P. (Hum. Mol. Genet. 2009) 3 4 22 64
  4. Association among IRF6 polymorphism, environmental factors, and nonsyndromic orofacial clefts in western china. (PMID: 19388848) Jia Z.L. … Shi B. (DNA Cell Biol. 2009) 3 22 46 64
  5. The association between interferon regulatory factor 6 (IRF6) and nonsyndromic cleft lip with or without cleft palate in a Honduran population. (PMID: 19536891) Diercks G.R. … Haddad J. (Laryngoscope 2009) 3 22 46 64

Products for IRF6 Gene

Sources for IRF6 Gene

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