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Aliases for WNT3 Gene

Aliases for WNT3 Gene

  • Wnt Family Member 3 2 3 5
  • Wingless-Type MMTV Integration Site Family, Member 3 2 3
  • Proto-Oncogene Int-4 Homolog 3 4
  • WNT-3 Proto-Oncogene Protein 2 3
  • INT4 3 4
  • Proto-Oncogene Wnt-3 3
  • TETAMS 3

External Ids for WNT3 Gene

Previous HGNC Symbols for WNT3 Gene

  • INT4

Previous GeneCards Identifiers for WNT3 Gene

  • GC17M044339
  • GC17M047240
  • GC17M045183
  • GC17M045316
  • GC17M042196
  • GC17M044839
  • GC17M040220

Summaries for WNT3 Gene

Entrez Gene Summary for WNT3 Gene

  • 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]

GeneCards Summary for WNT3 Gene

WNT3 (Wnt Family Member 3) is a Protein Coding gene. Diseases associated with WNT3 include Tetraamelia Syndrome, Autosomal Recessive and Nodular Basal Cell Carcinoma. Among its related pathways are Presynaptic function of Kainate receptors and Reelin Pathway (Cajal-Retzius cells). Gene Ontology (GO) annotations related to this gene include signaling receptor binding and frizzled binding. An important paralog of this gene is WNT3A.

UniProtKB/Swiss-Prot for WNT3 Gene

  • Ligand for members of the frizzled family of seven transmembrane receptors (Probable). Functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family (PubMed:26902720). Required for normal gastrulation, formation of the primitive streak, and for the formation of the mesoderm during early embryogenesis. Required for normal formation of the apical ectodermal ridge (By similarity). Required for normal embryonic development, and especially for limb development (PubMed:14872406).

Gene Wiki entry for WNT3 Gene

Additional gene information for WNT3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WNT3 Gene

Genomics for WNT3 Gene

GeneHancer (GH) Regulatory Elements for WNT3 Gene

Promoters and enhancers for WNT3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J046818 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 674.7 +12.5 12539 4.7 HDGF PKNOX1 ATF1 SIN3A ETS1 TCF12 POLR2B ZNF766 GATA2 ARID2 WNT3 KANSL1 ENSG00000262372 ARL17A EFCAB13 MRPL45P2 ARL17B RPS2P47 KPNB1 MAPK8IP1P1
GH17J046833 Promoter/Enhancer 1.3 EPDnew ENCODE 650.7 +0.0 12 0.2 ELF3 PKNOX1 ATF1 FOXA2 ZFP64 ARID4B KLF17 ZNF2 ATF7 CREM LOC101929777 WNT3 WNT9B RPS7P11
GH17J046834 Enhancer 0.2 ENCODE 650.7 -0.5 -536 0.2 LOC101929777 WNT3 WNT9B GOSR2 LINC01974
GH17J046922 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.8 -93.8 -93838 9.6 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 GOSR2 MRPL45P2 LOC101927060 ARL17B ARL17A EFCAB13 ENSG00000262372 CDC27 RPS7P11 MYL4
GH17J046769 Enhancer 1.5 FANTOM5 Ensembl ENCODE 14.5 +61.5 61452 4.6 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 KANSL1-AS1 ENSG00000262539 ARL17A WNT3 ENSG00000263766 ENSG00000253347 WNT9B KPNB1 GOSR2 MRPL45P2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around WNT3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the WNT3 gene promoter:
  • p53
  • HNF-4alpha2
  • HNF-4alpha1
  • E47
  • GATA-2
  • Nkx2-5
  • Pax-3
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for WNT3 Gene

Genomic Locations for WNT3 Gene
70,649 bases
Minus strand
70,649 bases
Minus strand

Genomic View for WNT3 Gene

Genes around WNT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WNT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WNT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WNT3 Gene

Proteins for WNT3 Gene

  • Protein details for WNT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Proto-oncogene Wnt-3
    Protein Accession:
    Secondary Accessions:
    • Q2M237
    • Q9H1J9

    Protein attributes for WNT3 Gene

    355 amino acids
    Molecular mass:
    39645 Da
    Quaternary structure:
    • Forms a soluble 1:1 complex with AFM; this prevents oligomerization and is required for prolonged biological activity (PubMed:26902720). The complex with AFM may represent the physiological form in body fluids (PubMed:26902720).Interacts with PORCN. Interacts with WLS (By similarity).

neXtProt entry for WNT3 Gene

Post-translational modifications for WNT3 Gene

  • Palmitoleoylation is required for efficient binding to frizzled receptors. Depalmitoleoylation leads to Wnt signaling pathway inhibition.
  • Glycosylation at isoforms=301 and isoforms=90
  • Modification sites at PhosphoSitePlus

Other Protein References for WNT3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for WNT3 Gene

Domains & Families for WNT3 Gene

Gene Families for WNT3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted secreted proteins

Protein Domains for WNT3 Gene

Suggested Antigen Peptide Sequences for WNT3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Wnt family.
  • Belongs to the Wnt family.
genes like me logo Genes that share domains with WNT3: view

Function for WNT3 Gene

Molecular function for WNT3 Gene

UniProtKB/Swiss-Prot Function:
Ligand for members of the frizzled family of seven transmembrane receptors (Probable). Functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family (PubMed:26902720). Required for normal gastrulation, formation of the primitive streak, and for the formation of the mesoderm during early embryogenesis. Required for normal formation of the apical ectodermal ridge (By similarity). Required for normal embryonic development, and especially for limb development (PubMed:14872406).
GENATLAS Biochemistry:
wingless-type MMTV integration site 3,Drosophila wingless (wg) segment polarity gene homolog,expressed in developing nervous system and in adult thalamus,cerebellum,pons,modulating cell fate and cell behavior during vertebrate development,required for the primary axis formation

LifeMap Function Summary for WNT3 Gene

During embryonic development, WNT3 as signaling molecule is secreted from the following cells
It affects the following cells:

Phenotypes From GWAS Catalog for WNT3 Gene

Gene Ontology (GO) - Molecular Function for WNT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding IEA --
GO:0005109 frizzled binding IPI 10557084
GO:0005515 protein binding IPI 18313787
GO:0019904 protein domain specific binding IEA --
GO:0048018 receptor ligand activity IDA 10557084
genes like me logo Genes that share ontologies with WNT3: view
genes like me logo Genes that share phenotypes with WNT3: view

Human Phenotype Ontology for WNT3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for WNT3 Gene

MGI Knock Outs for WNT3:
  • Wnt3 Wnt3<tm1Brd>
  • Wnt3 Wnt3<tm1Amc>
  • Wnt3 Wnt3<tm1Bhr>
  • Wnt3 Wnt3<tm2Brd>
  • Wnt3 Wnt3<tm2a(EUCOMM)Wtsi>

Animal Model Products

Clone Products

  • Addgene plasmids for WNT3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for WNT3 Gene

Localization for WNT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WNT3 Gene

Secreted, extracellular space, extracellular matrix. Secreted.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for WNT3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 5
golgi apparatus 4
nucleus 2
mitochondrion 1
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for WNT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space TAS 18313787
GO:0005737 cytoplasm IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005796 Golgi lumen TAS --
genes like me logo Genes that share ontologies with WNT3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for WNT3 Gene

Pathways & Interactions for WNT3 Gene

genes like me logo Genes that share pathways with WNT3: view

SIGNOR curated interactions for WNT3 Gene


Gene Ontology (GO) - Biological Process for WNT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis IMP 15588944
GO:0001707 mesoderm formation IEA --
GO:0007275 multicellular organism development IEA --
GO:0007276 gamete generation IEA --
GO:0007411 axon guidance IEA --
genes like me logo Genes that share ontologies with WNT3: view

Drugs & Compounds for WNT3 Gene

(9) Drugs for WNT3 Gene - From:

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FH535 Pharma Wnt/B-catenin inhibitor, Inhibitor of Wnt/beta-catenin signaling 0
ICG 001 Pharma Wnt/β-catenin pathway inhibitor 0
IWP 2 Pharma Wnt production inhibitor,PORCN inhibitor, PORCN inhibitor; inhibits Wnt processing and secretion 0
IWR-1-endo Pharma Potent Wnt signaling inhibitor 0
Kartogenin Pharma 0

(1) Additional Compounds for WNT3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with WNT3: view

Transcripts for WNT3 Gene

mRNA/cDNA for WNT3 Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(15) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for WNT3 Gene

Wingless-type MMTV integration site family, member 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for WNT3

Alternative Splicing Database (ASD) splice patterns (SP) for WNT3 Gene

No ASD Table

Relevant External Links for WNT3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for WNT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for WNT3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for WNT3 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x9.3), Skin - Sun Exposed (Lower leg) (x6.9), and Liver (x5.3).

Protein differential expression in normal tissues from HIPED for WNT3 Gene

This gene is overexpressed in Liver, secretome (65.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for WNT3 Gene

Protein tissue co-expression partners for WNT3 Gene

NURSA nuclear receptor signaling pathways regulating expression of WNT3 Gene:


SOURCE GeneReport for Unigene cluster for WNT3 Gene:


Evidence on tissue expression from TISSUES for WNT3 Gene

  • Skin(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for WNT3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • olfactory bulb
  • outer ear
  • pharynx
  • skull
  • breast
  • bronchus
  • chest wall
  • diaphragm
  • heart
  • lung
  • rib
  • rib cage
  • trachea
  • abdominal wall
  • adrenal gland
  • duodenum
  • intestine
  • kidney
  • large intestine
  • small intestine
  • spleen
  • stomach
  • anus
  • fallopian tube
  • pelvis
  • penis
  • placenta
  • rectum
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vulva
  • lower limb
  • upper limb
  • blood
  • blood vessel
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with WNT3: view

No data available for mRNA Expression by UniProt/SwissProt for WNT3 Gene

Orthologs for WNT3 Gene

This gene was present in the common ancestor of animals.

Orthologs for WNT3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia WNT3 34 33
  • 99.62 (n)
(Monodelphis domestica)
Mammalia WNT3 34
  • 99 (a)
(Canis familiaris)
Mammalia WNT3 34 33
  • 93.8 (n)
(Bos Taurus)
Mammalia WNT3 34 33
  • 92.58 (n)
(Mus musculus)
Mammalia Wnt3 16 34 33
  • 92.49 (n)
(Rattus norvegicus)
Mammalia Wnt3 33
  • 91.92 (n)
(Gallus gallus)
Aves WNT3 34 33
  • 83.76 (n)
(Anolis carolinensis)
Reptilia WNT3 34
  • 96 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia wnt3 33
  • 78.73 (n)
African clawed frog
(Xenopus laevis)
Amphibia wnt3a-A 33
(Danio rerio)
Actinopterygii wnt3 34 33
  • 78.66 (n)
fruit fly
(Drosophila melanogaster)
Insecta Wnt2 35
  • 46 (a)
Wnt6 35
  • 45 (a)
Wnt5 35
  • 41 (a)
(Caenorhabditis elegans)
Secernentea cwn-1 34 35
  • 38 (a)
egl-20 35
  • 35 (a)
lin-44 35
  • 31 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
Species where no ortholog for WNT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for WNT3 Gene

Gene Tree for WNT3 (if available)
Gene Tree for WNT3 (if available)
Evolutionary constrained regions (ECRs) for WNT3: view image

Paralogs for WNT3 Gene

Paralogs for WNT3 Gene

(18) SIMAP similar genes for WNT3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with WNT3: view

Variants for WNT3 Gene

Sequence variations from dbSNP and Humsavar for WNT3 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs104894653 pathogenic, Tetraamelia, autosomal recessive 46,773,743(-) G/A coding_sequence_variant, stop_gained
rs114693722 uncertain-significance, Tetraamelia, autosomal recessive 46,764,601(-) A/G 3_prime_UTR_variant
rs199742069 uncertain-significance, Tetraamelia, autosomal recessive 46,818,626(-) C/T 5_prime_UTR_variant
rs759600970 uncertain-significance, Tetraamelia, autosomal recessive 46,764,502(-) G/A/C 3_prime_UTR_variant
rs786205887 likely-pathogenic, Exstrophy of the bladder 46,773,719(-) A/C/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for WNT3 Gene

Variant ID Type Subtype PubMed ID
dgv1475n106 CNV deletion 24896259
dgv5668n54 CNV gain+loss 21841781
dgv5669n54 CNV gain+loss 21841781
dgv5670n54 CNV gain 21841781
dgv5671n54 CNV gain+loss 21841781
dgv5672n54 CNV gain 21841781
dgv5673n54 CNV loss 21841781
esv1005788 CNV deletion 20482838
esv1008863 CNV insertion 20482838
esv2656635 CNV deletion 23128226
esv2659354 CNV deletion 23128226
esv2758692 CNV gain+loss 17122850
esv28523 CNV loss 19812545
esv3435685 CNV insertion 20981092
esv3554487 CNV deletion 23714750
nsv1070832 CNV deletion 25765185
nsv1072742 CNV deletion 25765185
nsv1121937 CNV deletion 24896259
nsv1126465 CNV deletion 24896259
nsv1146669 OTHER inversion 26484159
nsv428343 CNV gain+loss 18775914
nsv483083 CNV gain 15286789
nsv575460 CNV gain+loss 21841781
nsv575461 CNV loss 21841781
nsv833465 CNV loss 17160897

Variation tolerance for WNT3 Gene

Residual Variation Intolerance Score: 16.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.20; 4.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for WNT3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WNT3 Gene

Disorders for WNT3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for WNT3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
tetraamelia syndrome, autosomal recessive
  • tetams
nodular basal cell carcinoma
  • basal cell carcinoma, nodular
bladder exstrophy-epispadias-cloacal exstrophy complex
  • eec
exstrophy of bladder
  • bladder exstrophy
klatskin's tumor
  • hilar cholangiocarcinoma
- elite association - COSMIC cancer census association via MalaCards
Search WNT3 in MalaCards View complete list of genes associated with diseases


  • Tetraamelia syndrome, autosomal recessive (TETAMS) [MIM:273395]: A rare human genetic disorder characterized by complete absence of all four limbs and other anomalies such as craniofacial, nervous system, pulmonary, skeletal and urogenital defects. {ECO:0000269 PubMed:14872406}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for WNT3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with WNT3: view

No data available for Genatlas for WNT3 Gene

Publications for WNT3 Gene

  1. Molecular cloning and chromosomal localization to 17q21 of the human WNT3 gene. (PMID: 8244403) Roelink H … Nusse R (Genomics 1993) 2 3 4 22 58
  2. Homozygous WNT3 mutation causes tetra-amelia in a large consanguineous family. (PMID: 14872406) Niemann S … Müller U (American journal of human genetics 2004) 3 4 22 58
  3. Molecular cloning and characterization of human WNT3. (PMID: 11604997) Katoh M (International journal of oncology 2001) 3 4 22 58
  4. Meta-analysis of Parkinson's disease: identification of a novel locus, RIT2. (PMID: 22451204) Pankratz N … PD GWAS Consortium (Annals of neurology 2012) 3 44 58
  5. Genome-wide association study identifies candidate genes for Parkinson's disease in an Ashkenazi Jewish population. (PMID: 21812969) Liu X … Lee JH (BMC medical genetics 2011) 3 44 58

Products for WNT3 Gene

Sources for WNT3 Gene

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