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

Gene ID: 57822, updated on 27-Nov-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
  • 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
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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)

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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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

Gene LinkOut

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