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IRF6 Gene(Protein Coding)

Interferon Regulatory Factor 6

GCID:
GC01M209785
GIFtS:
53
Genes Participants
UDN Logo

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 Popliteal Pterygium Syndrome and Van Der Woude Syndrome 1. Among its related pathways are Cytokine Signaling in Immune system and Primary Focal Segmental Glomerulosclerosis FSGS. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity. 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

Additional gene information 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

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for IRF6 Gene

Promoters and enhancers for IRF6 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01I209800 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 578.6 +0.3 255 10.2 HDGF PKNOX1 SMAD1 ARNT SIN3A FEZF1 ZNF2 YY1 POLR2B FOS IRF6 TRAF3IP3 DIEXF SYT14 LAMB3 C1orf74
GH01I209822 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 21.1 -19.6 -19587 6.5 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 DIEXF IRF6 SYT14 C1orf74 LOC101930114 TRAF3IP3
GH01I209782 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 20.7 +20.5 20528 6 HDGF FOXA2 PKNOX1 SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B C1orf74 TRAF3IP3 IRF6 SYT14
GH01I209814 Enhancer 1.5 VISTA FANTOM5 ENCODE dbSUPER 17.6 -9.9 -9922 3.9 CTCF SOX5 GATAD2A ZNF687 ZSCAN4 EBF1 MNT GABPA ETV4 TCF7 IRF6 C1orf74 LOC101930114 SYT14 LAMB3 DIEXF
GH01I209838 Enhancer 1.2 Ensembl ENCODE dbSUPER 20.6 -34.0 -33964 4.1 MXI1 FOXA2 JUN MAX RAD21 YY1 FOSL1 POLR2A SCRT2 HNF4G IRF6 SYT14 TRAF3IP3 DIEXF GC01M209934
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around IRF6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the IRF6 gene promoter:

Genomic Locations for IRF6 Gene

Genomic Locations for IRF6 Gene
chr1:209,785,623-209,806,175
(GRCh38/hg38)
Size:
20,553 bases
Orientation:
Minus strand
chr1:209,958,968-209,979,520
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for IRF6 Gene

Proteins for IRF6 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for IRF6 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

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

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for IRF6 Gene

Domains & Families for IRF6 Gene

Gene Families for IRF6 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for IRF6 Gene

InterPro:
Blocks:
ProtoNet:

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

Function for IRF6 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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).

Phenotypes From GWAS Catalog for IRF6 Gene

Gene Ontology (GO) - Molecular Function for IRF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding ISS --
GO:0003700 DNA binding transcription factor activity ISS --
GO:0005515 protein binding IPI 16049006
GO:0043565 sequence-specific DNA binding IDA 28473536
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

Clone Products

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nucleus (3)
See all subcellular structures

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:0030054 cell junction IDA --
GO:0070062 extracellular exosome IDA,HDA 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:0006366 transcription by RNA polymerase II IEA --
GO:0007050 cell cycle arrest IDA 18212048
GO:0008285 negative regulation of cell proliferation IDA 18212048
genes like me logo Genes that share ontologies with IRF6: view

No data available for SIGNOR curated interactions for IRF6 Gene

Drugs & Compounds for IRF6 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for IRF6 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for IRF6 Gene

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(196) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for IRF6 Gene

Interferon regulatory factor 6:
Representative Sequences:

Clone Products

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

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for IRF6 Gene
mRNA expression by BioGPS for IRF6 GenemRNA expression by GTEx 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
Regions:
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

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 33 34
  • 99.57 (n)
dog
(Canis familiaris)
 Mammalia IRF6 33 34
  • 93.94 (n)
cow
(Bos Taurus)
 Mammalia IRF6 33 34
  • 93.72 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia IRF6 34
  • 91 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Irf6 33
  • 90.65 (n)
mouse
(Mus musculus)
 Mammalia Irf6 33 16 34
  • 90.44 (n)
oppossum
(Monodelphis domestica)
 Mammalia IRF6 34
  • 87 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves IRF6 33 34
  • 78.36 (n)
lizard
(Anolis carolinensis)
 Reptilia IRF6 34
  • 84 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia irf6 33
  • 74.51 (n)
Str.6728 33
African clawed frog
(Xenopus laevis)
 Amphibia xIRF-6 33
zebrafish
(Danio rerio)
 Actinopterygii irf6 33 34
  • 69.38 (n)
zgc63500 33
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

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for IRF6 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1044516 benign, Popliteal pterygium syndrome, Cleft Lip +/- Cleft Palate, Autosomal Dominant, Van der Woude syndrome 209,786,269(-) G/T 3_prime_UTR_variant
rs1060499555 pathogenic, Van der Woude syndrome 209,801,301(-) A/G coding_sequence_variant, intron_variant, missense_variant
rs112896538 likely-benign, Popliteal pterygium syndrome, Cleft Lip +/- Cleft Palate, Autosomal Dominant, Van der Woude syndrome 209,786,006(-) C/T 3_prime_UTR_variant
rs114756064 likely-benign, Van der Woude syndrome, Cleft Lip +/- Cleft Palate, Autosomal Dominant, Popliteal pterygium syndrome 209,786,909(-) G/A 3_prime_UTR_variant
rs121434224 pathogenic, Van der Woude syndrome 209,796,453(-) C/A 5_prime_UTR_variant, coding_sequence_variant, stop_gained

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)

Additional Variant Information for IRF6 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for IRF6 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
popliteal pterygium syndrome
  • pps
van der woude syndrome 1
  • vws1
orofacial cleft 6
  • orofacial cleft 6, susceptibility to
tooth agenesis
  • familial tooth agenesis
isolated cleft lip
- 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.

Additional Disease Information for IRF6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 JC (Nature genetics 2002) 2 3 4 22 58
  2. Lack of association between IRF6 polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian population. (PMID: 19780991) Paranaíba LM … Coletta RD (Oral diseases 2010) 3 22 44 58
  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 HJ … Shore P (Human molecular genetics 2009) 3 4 22 58
  4. Association among IRF6 polymorphism, environmental factors, and nonsyndromic orofacial clefts in western china. (PMID: 19388848) Jia ZL … Shi B (DNA and cell biology 2009) 3 22 44 58
  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 GR … Haddad J (The Laryngoscope 2009) 3 22 44 58

Products for IRF6 Gene

Sources for IRF6 Gene

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