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

Summary

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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dual role of GRHL3 in bladder carcinogenesis depending on histological subtypes.
Title: Dual role of GRHL3 in bladder carcinogenesis depending on histological subtypes.
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.
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.
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.
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.
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.
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.
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.
Grainyhead-Like 3 Influences Migration and Invasion of Urothelial Carcinoma Cells.
Title: Grainyhead-Like 3 Influences Migration and Invasion of Urothelial Carcinoma Cells.
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	not available

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 EBI GWAS CatalogPubMed

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

SHGC-149508 (e-PCR)
- UniSTS:177046

SHGC-74407 (e-PCR)
- UniSTS:74166

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

NG_009308.2 RefSeqGene

Range

4967..40928

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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