Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	57822
Gene name Gene Name - the full gene name approved by the HGNC.	Grainyhead like transcription factor 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	GRHL3
Synonyms (NCBI Gene) Gene synonyms aliases	SOM, TFCP2L4, VWS2
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p36.11
Summary Summary of gene provided in NCBI Entrez Gene.	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 encod

Show/Hide all(12)

SNP ID	Visualize variation	Clinical significance	Consequence
rs752673677	G>A	Pathogenic	Coding sequence variant, missense variant
rs770938921	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs797044857	C>G	Likely-pathogenic	Missense variant, coding sequence variant, intron variant
rs879255243	GGAG>-	Pathogenic	Coding sequence variant, frameshift variant
rs879255244	G>T	Pathogenic	Splice donor variant
rs879255245	C>T	Pathogenic	Missense variant, coding sequence variant
rs879255573	->GT	Pathogenic	Coding sequence variant, frameshift variant
rs886037767	C>T	Pathogenic	Synonymous variant, coding sequence variant
rs886037768	G>T	Pathogenic	Splice donor variant
rs886037769	->C	Pathogenic	Frameshift variant, coding sequence variant
rs886037770	T>-	Pathogenic	Splice donor variant
rs1553172687	G>A	Pathogenic	Coding sequence variant, stop gained

Show/Hide all(73)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017699	hsa-miR-335-5p	Microarray	18185580
MIRT1034113	hsa-miR-1266	CLIP-seq
MIRT1034114	hsa-miR-1297	CLIP-seq
MIRT1034115	hsa-miR-1305	CLIP-seq
MIRT1034116	hsa-miR-147	CLIP-seq
MIRT1034117	hsa-miR-1827	CLIP-seq
MIRT1034118	hsa-miR-185	CLIP-seq
MIRT1034119	hsa-miR-194	CLIP-seq
MIRT1034120	hsa-miR-26a	CLIP-seq
MIRT1034121	hsa-miR-26b	CLIP-seq
MIRT1034122	hsa-miR-335	CLIP-seq
MIRT1034123	hsa-miR-3910	CLIP-seq
MIRT1034124	hsa-miR-3911	CLIP-seq
MIRT1034125	hsa-miR-4270	CLIP-seq
MIRT1034126	hsa-miR-4306	CLIP-seq
MIRT1034127	hsa-miR-4441	CLIP-seq
MIRT1034128	hsa-miR-4465	CLIP-seq
MIRT1034129	hsa-miR-4491	CLIP-seq
MIRT1034130	hsa-miR-4518	CLIP-seq
MIRT1034131	hsa-miR-4644	CLIP-seq
MIRT1034132	hsa-miR-4649-3p	CLIP-seq
MIRT1034133	hsa-miR-4657	CLIP-seq
MIRT1034134	hsa-miR-4747-5p	CLIP-seq
MIRT1034135	hsa-miR-498	CLIP-seq
MIRT1034136	hsa-miR-642a	CLIP-seq
MIRT1034137	hsa-miR-644	CLIP-seq
MIRT1034138	hsa-miR-802	CLIP-seq
MIRT1034139	hsa-miR-1207-5p	CLIP-seq
MIRT1034140	hsa-miR-1236	CLIP-seq
MIRT1034113	hsa-miR-1266	CLIP-seq
MIRT1034114	hsa-miR-1297	CLIP-seq
MIRT1034116	hsa-miR-147	CLIP-seq
MIRT1034117	hsa-miR-1827	CLIP-seq
MIRT1034118	hsa-miR-185	CLIP-seq
MIRT1034119	hsa-miR-194	CLIP-seq
MIRT1034120	hsa-miR-26a	CLIP-seq
MIRT1034121	hsa-miR-26b	CLIP-seq
MIRT1034141	hsa-miR-3127-5p	CLIP-seq
MIRT1034142	hsa-miR-3612	CLIP-seq
MIRT1034123	hsa-miR-3910	CLIP-seq
MIRT1034125	hsa-miR-4270	CLIP-seq
MIRT1034126	hsa-miR-4306	CLIP-seq
MIRT1034143	hsa-miR-4420	CLIP-seq
MIRT1034144	hsa-miR-4427	CLIP-seq
MIRT1034127	hsa-miR-4441	CLIP-seq
MIRT1034128	hsa-miR-4465	CLIP-seq
MIRT1034145	hsa-miR-4468	CLIP-seq
MIRT1034129	hsa-miR-4491	CLIP-seq
MIRT1034130	hsa-miR-4518	CLIP-seq
MIRT1034131	hsa-miR-4644	CLIP-seq
MIRT1034132	hsa-miR-4649-3p	CLIP-seq
MIRT1034133	hsa-miR-4657	CLIP-seq
MIRT1034146	hsa-miR-4711-5p	CLIP-seq
MIRT1034147	hsa-miR-4736	CLIP-seq
MIRT1034134	hsa-miR-4747-5p	CLIP-seq
MIRT1034148	hsa-miR-4763-3p	CLIP-seq
MIRT1034135	hsa-miR-498	CLIP-seq
MIRT1034136	hsa-miR-642a	CLIP-seq
MIRT1034149	hsa-miR-650	CLIP-seq
MIRT1034138	hsa-miR-802	CLIP-seq
MIRT2006735	hsa-miR-1539	CLIP-seq
MIRT2006736	hsa-miR-3193	CLIP-seq
MIRT1034114	hsa-miR-1297	CLIP-seq
MIRT2239098	hsa-miR-132	CLIP-seq
MIRT2239099	hsa-miR-212	CLIP-seq
MIRT1034120	hsa-miR-26a	CLIP-seq
MIRT1034121	hsa-miR-26b	CLIP-seq
MIRT2239100	hsa-miR-3132	CLIP-seq
MIRT2239101	hsa-miR-3182	CLIP-seq
MIRT2239102	hsa-miR-4314	CLIP-seq
MIRT1034128	hsa-miR-4465	CLIP-seq
MIRT1034135	hsa-miR-498	CLIP-seq
MIRT1034138	hsa-miR-802	CLIP-seq

Show/Hide all(41)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IBA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	23685552
GO:0001736	Process	Establishment of planar polarity	IEA
GO:0001843	Process	Neural tube closure	IEA
GO:0001843	Process	Neural tube closure	ISS
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005515	Function	Protein binding	IPI	23455924, 32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	21081122
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005829	Component	Cytosol	IDA
GO:0005929	Component	Cilium	IDA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0006366	Process	Transcription by RNA polymerase II	IEA
GO:0007389	Process	Pattern specification process	IEA
GO:0007398	Process	Ectoderm development	IEA
GO:0007417	Process	Central nervous system development	IEA
GO:0008544	Process	Epidermis development	IEA
GO:0008544	Process	Epidermis development	ISS
GO:0010467	Process	Gene expression	IEA
GO:0010628	Process	Positive regulation of gene expression	IEA
GO:0015629	Component	Actin cytoskeleton	IDA
GO:0031490	Function	Chromatin DNA binding	IDA	21081122
GO:0032956	Process	Regulation of actin cytoskeleton organization	IGI	20643356
GO:0042060	Process	Wound healing	IEA
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0043565	Function	Sequence-specific DNA binding	ISS
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	23685552
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0061029	Process	Eyelid development in camera-type eye	IEA
GO:0061436	Process	Establishment of skin barrier	IEA
GO:0090103	Process	Cochlea morphogenesis	IEA

MIM	HGNC	e!Ensembl
608317	25839	ENSG00000158055

Protein

UniProt ID

Q8TE85

Protein name

Grainyhead-like protein 3 homolog (Sister of mammalian grainyhead) (Transcription factor CP2-like 4)

Protein function

Transcription factor playing important roles in primary neurulation and in the differentiation of stratified epithelia of both ectodermal and endodermal origin (By similarity). Binds directly to the consensus DNA sequence 5'-AACCGGTT-3' acting a

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04516	CP2	213 → 421	CP2 transcription factor	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in brain, colon, pancreas, placenta and kidney. Isoform 1 is expressed in lung and tonsil. Isoform 2 is prostate-specific. {ECO:0000269|PubMed:12549979}.

Sequence

MSNELDFRSVRLLKNDPVNLQKFSYTSEDEAWKTYLENPLTAATKAMMRVNGDDDSVAAL
SFLYDYYMGPKEKRILSSSTGGRNDQGKRYYHGMEYETDLTPLESPTHLMKFLTENVSGT
PEYPDLLKKNNLMSLEGALPTPGKAAPLPAGPSKLEAGSVDSYLLPTTDMYDNGSLNSLF
ESIHGVPPTQRWQPDSTFKDDPQESMLFPDILKTSPEPPCPEDYPSLKSDFEYTLGSPKA
IHIKSGESPMAYLNKGQFYPVTLRTPAGGKGLALSSNKVKSVVMVVFDNEKVPVEQLRFW
KHWHSRQPTAKQRVIDVADCKENFNTVEHIEEVAYNALSFVWNVNEEAKVFIGVNCLSTD
FSSQKGVKGVPLNLQIDTYDCGLGTERLVHRAVCQIKIFCDKGAERKMRDDERKQFRRKV
KCPDSSNSGVKGCLLSGFRGNETTYLRPETDLETPPVLFIPNVHFSSLQRSGGAAPSAGP
SSSNRLPLKRTCSPFTEEFEPLPSKQAKEGDLQRVLLYVRRETEEVFDALMLKTPDLKGL
RNAISEKYGFPEENIYKVYKKCKRGETSLLHPRLSRHPPPDCLECSHPVTQVRNMGFGDG
FWRQRDLDSNPSPTTVNSLHFTVNSE

Sequence length

626

Interactions

View interactions

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Van Der Woude Syndrome	van der woude syndrome 2	rs879255245, rs1553172687, rs879255573, rs879255243, rs752673677, rs879255244	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Psoriasis	Psoriasis	N/A	N/A	GWAS
Psoriasis vulgaris	Psoriasis vulgaris	N/A	N/A	GWAS
Systemic lupus erythematosus	Systemic lupus erythematosus	N/A	N/A	GWAS

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Barrett Esophagus	Associate	29906417
Breast Neoplasms	Associate	24363083
Carcinoma	Associate	26837418
Cleft Palate	Associate	27459192, 31172578, 34459660
Lymphoma Large B Cell Diffuse	Associate	26797800
Neoplasms	Inhibit	24363083, 29301499
Neoplasms	Associate	26837418
Nonsyndromic Holoprosencephaly	Associate	27459192
Orofacial Cleft 1	Associate	27018475, 27459192, 34459660, 36901693
Otofaciocervical Syndrome	Associate	36901693
Sertoli Cell Only Syndrome	Associate	26797800
Skin Neoplasms	Inhibit	29301499
Skin Neoplasms	Associate	29301499
Triple Negative Breast Neoplasms	Associate	24363083
Van der Woude syndrome	Associate	27018475, 27459192, 36901693
Van der Woude syndrome 2	Associate	36901693

GRHL3 (grainyhead like transcription factor 3)