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    GRHL3 grainyhead like transcription factor 3 [ Homo sapiens (human) ]

    Gene ID: 57822, updated on 28-Oct-2024

    Summary

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    Official Symbol
    GRHL3provided by HGNC
    Official Full Name
    grainyhead like transcription factor 3provided by HGNC
    Primary source
    HGNC:HGNC:25839
    See related
    Ensembl:ENSG00000158055 MIM:608317; AllianceGenome:HGNC:25839
    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
    SOM; VWS2; TFCP2L4
    Summary
    This gene encodes a member of the grainyhead family of transcription factors. The encoded protein may function as a transcription factor during development, and has been shown to stimulate migration of endothelial cells. Multiple transcript variants encoding distinct isoforms have been identified for this gene.[provided by RefSeq, Aug 2010]
    Expression
    Biased expression in esophagus (RPKM 31.7), skin (RPKM 14.0) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See GRHL3 in Genome Data Viewer
    Location:
    1p36.11
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (24319357..24364482)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (24157463..24202842)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (24645847..24690972)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903879 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:24480583-24481180 Neighboring gene interferon lambda receptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 391 Neighboring gene long intergenic non-protein coding RNA 2800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24581311-24581877 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24604941-24605442 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24612590-24613188 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24613189-24613787 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24624394-24624641 Neighboring gene Sharpr-MPRA regulatory region 347 Neighboring gene GRHL3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 432 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24648587-24649104 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:24649105-24649620 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:24661406-24662028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24664014-24664642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24664643-24665269 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24669049-24669863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 396 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:24691307-24692506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 398 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24714266-24714492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 399 Neighboring gene sperm tail PG-rich repeat containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 400 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:24745074-24746273 Neighboring gene NIPA like domain containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24782303-24782815 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:24784099-24784600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 402 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24828715-24828887 Neighboring gene RCAN3 antisense RNA Neighboring gene RCAN family member 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Dual role of GRHL3 in bladder carcinogenesis depending on histological subtypes. Lammert FC, et al. Mol Oncol, 2024 Jun. PMID 38429970, Free PMC Article
    2. Sequencing the GRHL3 Coding Region Reveals Rare Truncating Mutations and a Common Susceptibility Variant for Nonsyndromic Cleft Palate. Mangold E, et al. Am J Hum Genet, 2016 Apr 7. PMID 27018475, Free PMC Article
    3. Association study between Van der Woude Syndrome causative gene GRHL3 and nonsyndromic cleft lip with or without cleft palate in a Chinese cohort. Wang Y, et al. Gene, 2016 Aug 15. PMID 27129939
    4. Lack of Association between Missense Variants in GRHL3 (rs2486668 and rs545809) and Susceptibility to Non-Syndromic Orofacial Clefts in a Han Chinese Population. He M, et al. PLoS One, 2016. PMID 27459192, Free PMC Article
    5. Rare deleterious variants in GRHL3 are associated with human spina bifida. Lemay P, et al. Hum Mutat, 2017 Jun. PMID 28276201

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dual role of GRHL3 in bladder carcinogenesis depending on histological subtypes.
      Title: Dual role of GRHL3 in bladder carcinogenesis depending on histological subtypes.
    2. The GRHL3-regulated long non-coding RNA lnc-DC modulates keratinocytes differentiation by interacting with IGF2BP2 and up-regulating ZNF750.
      Title: The GRHL3-regulated long non-coding RNA lnc-DC modulates keratinocytes differentiation by interacting with IGF2BP2 and up-regulating ZNF750.
    3. A Comprehensive Genetic Analysis of Slovenian Families with Multiple Cases of Orofacial Clefts Reveals Novel Variants in the Genes IRF6, GRHL3, and TBX22.
      Title: A Comprehensive Genetic Analysis of Slovenian Families with Multiple Cases of Orofacial Clefts Reveals Novel Variants in the Genes IRF6, GRHL3, and TBX22.
    4. Association analysis of SNPs in GRHL3, FAF1, and KCNJ2 with NSCPO sub-phenotypes in Han Chinese.
      Title: Association analysis of SNPs in GRHL3, FAF1, and KCNJ2 with NSCPO sub-phenotypes in Han Chinese.
    5. Novel GRHL3 Variants in a South African Cohort With Cleft Lip and Palate.
      Title: Novel GRHL3 Variants in a South African Cohort With Cleft Lip and Palate.
    6. GRHL3 Promotes Tumor Growth and Metastasis via the MEK Pathway in Colorectal Cancer.
      Title: GRHL3 Promotes Tumor Growth and Metastasis via the MEK Pathway in Colorectal Cancer.
    7. Genetic markers for non-syndromic orofacial clefts in populations of European ancestry: a meta-analysis.
      Title: Genetic markers for non-syndromic orofacial clefts in populations of European ancestry: a meta-analysis.
    8. The functional GRHL3-filaggrin axis maintains a tumor differentiation potential and influences drug sensitivity.
      Title: The functional GRHL3-filaggrin axis maintains a tumor differentiation potential and influences drug sensitivity.
    9. Grainyhead-Like 3 Influences Migration and Invasion of Urothelial Carcinoma Cells.
      Title: Grainyhead-Like 3 Influences Migration and Invasion of Urothelial Carcinoma Cells.
    10. Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration.
      Title: Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    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

    Associated conditions

    Description Tests
    Van der Woude syndrome 2
    MedGen: C1847604 OMIM: 606713 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC46624

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in central nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cochlea morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ectoderm development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in epidermis development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in establishment of planar polarity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment of skin barrier IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in eyelid development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neural tube closure ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in pattern specification process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of actin cytoskeleton organization IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in wound healing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    grainyhead-like protein 3 homolog
    Names
    sister of mammalian grainyhead
    transcription factor CP2-like 4
    transcription factor hSOM1

    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_009308.2 RefSeqGene

      Range
      4967..40928
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001195010.2 → NP_001181939.1  grainyhead-like protein 3 homolog isoform 4

      See identical proteins and their annotated locations for NP_001181939.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) 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 (4) is shorter than isoform 1.
      Source sequence(s)
      AL138902, BC036890
      Consensus CDS
      CCDS53284.1
      UniProtKB/Swiss-Prot
      Q8TE85
      Related
      ENSP00000348333.2, ENST00000356046.6
      Conserved Domains (1) summary
      pfam04516
      Location:164 → 375
      CP2; CP2 transcription factor

    2. NM_021180.4 → NP_067003.2  grainyhead-like protein 3 homolog isoform 1

      See identical proteins and their annotated locations for NP_067003.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as SOM1) encodes isoform 1.
      Source sequence(s)
      AK315164, AY231160, BC036890
      Consensus CDS
      CCDS251.1
      UniProtKB/Swiss-Prot
      Q8TE85
      Related
      ENSP00000236255.4, ENST00000236255.4
      Conserved Domains (1) summary
      pfam04516
      Location:215 → 426
      CP2; CP2 transcription factor

    3. NM_198173.3 → NP_937816.1  grainyhead-like protein 3 homolog isoform 2

      See identical proteins and their annotated locations for NP_937816.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as SOM2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK315164, AY231160, BC036890, DA714132
      Consensus CDS
      CCDS44088.1
      UniProtKB/Swiss-Prot
      Q8TE85
      Related
      ENSP00000354943.5, ENST00000361548.9
      Conserved Domains (1) summary
      pfam04516
      Location:210 → 421
      CP2; CP2 transcription factor

    4. NM_198174.3 → NP_937817.3  grainyhead-like protein 3 homolog isoform 3

      See identical proteins and their annotated locations for NP_937817.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has distinct N- and C-termini and is longer than isoform 1.
      Source sequence(s)
      AK074386, AK315164, DA714132
      Consensus CDS
      CCDS252.2
      UniProtKB/Swiss-Prot
      A2A297, B2RCL1, G3XAF0, Q5TH78, Q86Y06, Q8N407, Q8TE85
      Related
      ENSP00000288955.5, ENST00000350501.9
      Conserved Domains (1) summary
      pfam04516
      Location:210 → 421
      CP2; CP2 transcription factor

    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
      24319357..24364482
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541870.3 → XP_011540172.1  grainyhead-like protein 3 homolog isoform X2

      See identical proteins and their annotated locations for XP_011540172.1

      UniProtKB/Swiss-Prot
      Q8TE85
      Related
      ENSP00000509790.1, ENST00000692334.1
      Conserved Domains (1) summary
      pfam04516
      Location:117 → 328
      CP2; CP2 transcription factor

    2. XM_011541869.2 → XP_011540171.1  grainyhead-like protein 3 homolog isoform X1

      See identical proteins and their annotated locations for XP_011540171.1

      UniProtKB/Swiss-Prot
      Q8TE85
      Related
      ENSP00000431290.2, ENST00000524724.6
      Conserved Domains (1) summary
      pfam04516
      Location:164 → 375
      CP2; CP2 transcription factor

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      24157463..24202842
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337935.1 → XP_054193910.1  grainyhead-like protein 3 homolog isoform X2

    2. XM_054337934.1 → XP_054193909.1  grainyhead-like protein 3 homolog isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TE85.3 GenPept UniProtKB/Swiss-Prot:Q8TE85

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

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