WNT3 Wnt family member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: WNT3provided by HGNC
Official Full Name: Wnt family member 3provided by HGNC
Primary source: HGNC:HGNC:12782
See related: Ensembl:ENSG00000108379 MIM:165330; AllianceGenome:HGNC:12782
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: INT4; TETAMS
Summary: The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It encodes a protein which shows 98% amino acid identity to mouse Wnt3 protein, and 84% to human WNT3A protein, another WNT gene product. The mouse studies show the requirement of Wnt3 in primary axis formation in the mouse. Studies of the gene expression suggest that this gene may play a key role in some cases of human breast, rectal, lung, and gastric cancer through activation of the WNT-beta-catenin-TCF signaling pathway. This gene is clustered with WNT15, another family member, in the chromosome 17q21 region. [provided by RefSeq, Jul 2008]
Expression: Biased expression in skin (RPKM 21.7), testis (RPKM 3.1) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q21.31-q21.32

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (46762506..46818692, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (47623975..47680171, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (44839872..44896058, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LINC01023 Promotes the Hepatoblastoma Tumorigenesis via miR-378a-5p/WNT3 Axis.
Title: LINC01023 Promotes the Hepatoblastoma Tumorigenesis via miR-378a-5p/WNT3 Axis.
Four Genes Predictive for the Severity of Hematological Damage Reveal a Similar Response after X Irradiation and Chemotherapy.
Title: Four Genes Predictive for the Severity of Hematological Damage Reveal a Similar Response after X Irradiation and Chemotherapy.
WNT3 hypomethylation counteracts low activity of the Wnt signaling pathway in the placenta of preeclampsia.
Title: WNT3 hypomethylation counteracts low activity of the Wnt signaling pathway in the placenta of preeclampsia.
Concurrent Wnt pathway component expression in breast and colorectal cancer.
Title: Concurrent Wnt pathway component expression in breast and colorectal cancer.
Identification of candidate lncRNAs and circRNAs regulating WNT3/beta-catenin signaling in essential hypertension.
Title: Identification of candidate lncRNAs and circRNAs regulating WNT3/β-catenin signaling in essential hypertension.
Circulating miR-374b-5p negatively regulates osteoblast differentiation in the progression of osteoporosis via targeting Wnt3 AND Runx2.
Title: Circulating miR-374b-5p negatively regulates osteoblast differentiation in the progression of osteoporosis via targeting Wnt3 AND Runx2.
Based on the findings of our current study, the rs3809857 and rs9890413 polymorphisms of WNT3 appeared to be associated with non-syndromic cleft lip (CL) with or without cleft palate (NSCL/P) . Limited evidence is found to support the association between other WNT3 polymorphisms and risk of NSCL/P.
Title: Association of the WNT3 polymorphisms and non-syndromic cleft lip with or without cleft palate: evidence from a meta-analysis.
The importance of the SPAG5/AKT-mTOR/Wnt3 axis identified in BUC cell models.
Title: SPAG5 promotes proliferation and suppresses apoptosis in bladder urothelial carcinoma by upregulating Wnt3 via activating the AKT/mTOR pathway and predicts poorer survival.
Demonstrate a significant change in miRNA profile dependent on the assisted reproductive technology outcome affecting Wnt pathway.
Title: Altered miRNA-profile dependent on ART outcome in early pregnancy targets Wnt-pathway.
High expression of WNT3 is associated with hepatocellular carcinoma.
Title: miR-1247-5p functions as a tumor suppressor in human hepatocellular carcinoma by targeting Wnt3.

Submit: New GeneRIF Correction See all GeneRIFs (45)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Tetraamelia syndrome 1 MedGen: C4012268 OMIM: 273395 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genome-wide association study identifies candidate genes for Parkinson's disease in an Ashkenazi Jewish population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of a novel Parkinson's disease locus via stratified genome-wide association study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of Parkinson's disease: identification of a novel locus, RIT2. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multiple common variants for celiac disease influencing immune gene expression. 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

WI-10450 (e-PCR)
- UniSTS:10012

NoName (e-PCR)
- UniSTS:483409

G17967 (e-PCR)
- UniSTS:69730

Wnt3 (e-PCR), detects polymorphism
- UniSTS:516492

GDB:196138 (e-PCR)
- UniSTS:155819

D17S728 (e-PCR)
- UniSTS:147138

NoName (e-PCR)
- UniSTS:480460

D17S791 (e-PCR)
- UniSTS:54990

D17S791 (e-PCR)
- UniSTS:59889

G17970 (e-PCR)
- UniSTS:3581

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cytokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables frizzled binding	IBA Inferred from Biological aspect of Ancestor more info
enables frizzled binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables receptor ligand activity	IC Inferred by Curator more info	PubMed
enables receptor ligand activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Spemann organizer formation at the anterior end of the primitive streak	IEA Inferred from Electronic Annotation more info
involved_in anterior/posterior axis specification	IEA Inferred from Electronic Annotation more info
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in canonical Wnt signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to retinoic acid	ISS Inferred from Sequence or Structural Similarity more info
involved_in dorsal/ventral axis specification	IEA Inferred from Electronic Annotation more info
involved_in embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic hindlimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in gamete generation	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in head morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in limb bud formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mammary gland epithelium development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mesoderm formation	IEA Inferred from Electronic Annotation more info
involved_in midbrain dopaminergic neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of axon extension involved in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of collateral sprouting in absence of injury	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of osteoblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mesenchymal stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi lumen	TAS Traceable Author Statement more info
part_of Wnt signalosome	IC Inferred by Curator more info	PubMed
part_of Wnt signalosome	NAS Non-traceable Author Statement more info	PubMed
located_in endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular exosome	TAS Traceable Author Statement more info
located_in extracellular matrix	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	TAS Traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: proto-oncogene Wnt-3

Names: WNT-3 proto-oncogene protein; proto-oncogene Int-4 homolog; wingless-type MMTV integration site family, member 3

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.