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Aliases for WNT3A Gene

Aliases for WNT3A Gene

  • Wnt Family Member 3A 2 3 5
  • Wingless-Type MMTV Integration Site Family, Member 3A 2 3
  • Protein Wnt-3a 3

External Ids for WNT3A Gene

Previous GeneCards Identifiers for WNT3A Gene

  • GC01P226691
  • GC01P223933
  • GC01P224580
  • GC01P225169
  • GC01P224501
  • GC01P226261
  • GC01P228194
  • GC01P198726

Summaries for WNT3A Gene

Entrez Gene Summary for WNT3A 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 96% amino acid identity to mouse Wnt3A protein, and 84% to human WNT3 protein, another WNT gene product. This gene is clustered with WNT14 gene, another family member, in chromosome 1q42 region. [provided by RefSeq, Jul 2008]

GeneCards Summary for WNT3A Gene

WNT3A (Wnt Family Member 3A) is a Protein Coding gene. Diseases associated with WNT3A include Osteoporosis, Juvenile and Diarrhea 4, Malabsorptive, Congenital. Among its related pathways are Presynaptic function of Kainate receptors and Hematopoietic Stem Cell Differentiation Pathways and Lineage-specific Markers. Gene Ontology (GO) annotations related to this gene include signaling receptor binding and protein domain specific binding. An important paralog of this gene is WNT3.

UniProtKB/Swiss-Prot for WNT3A 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:20093360, PubMed:21244856, PubMed:24841207, PubMed:26902720). Required for normal embryonic mesoderm development and formation of caudal somites. Required for normal morphogenesis of the developing neural tube (By similarity). Mediates self-renewal of the stem cells at the bottom on intestinal crypts (in vitro) (PubMed:26902720).

Gene Wiki entry for WNT3A Gene

Additional gene information for WNT3A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WNT3A Gene

Genomics for WNT3A Gene

GeneHancer (GH) Regulatory Elements for WNT3A Gene

Promoters and enhancers for WNT3A 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
GH01J228006 Promoter 0.8 EPDnew 650.7 0.0 -43 0.1 ZFP69B ZNF692 KLF17 KLF14 ZBTB26 EZH2 WNT3A SEPT14P17
GH01J228081 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.6 +79.5 79533 10.7 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ARF1 CICP26 ENSG00000269890 ZNF678 C1orf35 OBSCN CDC42BPA WNT3A ENSG00000269934 OBSCN-AS1
GH01J227942 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 10.9 -61.3 -61305 6 ARNT SIN3A ZNF2 ZBTB7B ZNF48 YY1 ZNF121 GLIS2 ELK1 ARID2 WNT9A OBSCN-AS1 WNT3A OBSCN IBA57 ENSG00000269934 MRPL55 MIR5008
GH01J227761 Enhancer 1.4 Ensembl ENCODE dbSUPER 10 -243.8 -243776 3.4 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A ZNF2 ZNF48 GLIS2 ZNF213 WNT3A SNAP47 SNAP47-AS1 LOC105373289
GH01J227909 Enhancer 0.8 FANTOM5 ENCODE 16.6 -96.3 -96316 1.8 KLF1 SP3 ZNF280D KLF17 NFXL1 MITF ZFHX2 ZNF341 WT1 ZBTB17 WNT3A MIR5008 PRSS38
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around WNT3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the WNT3A gene promoter:
  • AP-1
  • NF-kappaB1
  • NF-kappaB
  • HNF-4alpha1
  • C/EBPalpha
  • c-Jun
  • ATF-2
  • GATA-1

Genomic Locations for WNT3A Gene

Genomic Locations for WNT3A Gene
59,690 bases
Plus strand
54,250 bases
Plus strand

Genomic View for WNT3A Gene

Genes around WNT3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WNT3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WNT3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WNT3A Gene

Proteins for WNT3A Gene

  • Protein details for WNT3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Wnt-3a
    Protein Accession:
    Secondary Accessions:
    • Q3SY79
    • Q3SY80
    • Q969P2

    Protein attributes for WNT3A Gene

    352 amino acids
    Molecular mass:
    39365 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). Homooligomer; disulfide-linked, leading to inactivation (By similarity). Interacts with PORCN (PubMed:20826466). Interacts with APCDD1 and WLS (PubMed:16678095, PubMed:20393562). Component of the Wnt-Fzd-LRP5-LRP6 signaling complex that contains a WNT protein, a FZD protein and LRP5 or LRP6. Interacts directly in the complex with LRP6 (PubMed:20093360).

    Alternative splice isoforms for WNT3A Gene


neXtProt entry for WNT3A Gene

Post-translational modifications for WNT3A Gene

  • Palmitoleoylation by PORCN is required for efficient binding to frizzled receptors. Palmitoleoylation is required for proper trafficking to cell surface, vacuolar acidification is critical to release palmitoleoylated WNT3A from WLS in secretory vesicles (PubMed:20826466, PubMed:21244856, PubMed:24292069). Depalmitoleoylated by NOTUM, leading to inhibit Wnt signaling pathway, possibly by promoting disulfide bond formation and oligomerization (PubMed:25731175).
  • Proteolytic processing by TIKI1 and TIKI2 promotes oxidation and formation of large disulfide-bond oligomers, leading to inactivation of WNT3A.
  • Disulfide bonds have critical and distinct roles in secretion and activity. Loss of each conserved cysteine in WNT3A results in high molecular weight oxidized Wnt oligomers, which are formed through inter-Wnt disulfide bonding.
  • Glycosylation at isoforms=2298 and posLast=8787
  • Modification sites at PhosphoSitePlus

Other Protein References for WNT3A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for WNT3A Gene

Domains & Families for WNT3A Gene

Gene Families for WNT3A Gene

Protein Domains for WNT3A Gene

Suggested Antigen Peptide Sequences for WNT3A 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 WNT3A: view

Function for WNT3A Gene

Molecular function for WNT3A 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:20093360, PubMed:21244856, PubMed:24841207, PubMed:26902720). Required for normal embryonic mesoderm development and formation of caudal somites. Required for normal morphogenesis of the developing neural tube (By similarity). Mediates self-renewal of the stem cells at the bottom on intestinal crypts (in vitro) (PubMed:26902720).

LifeMap Function Summary for WNT3A Gene

During embryonic development, WNT3A as signaling molecule is secreted from the following cells
WNT3A as growth factor is involved in stem cell differentiation protocols towards the derivation of the following cells:

Phenotypes From GWAS Catalog for WNT3A Gene

Gene Ontology (GO) - Molecular Function for WNT3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity ISS,IEA --
GO:0005102 signaling receptor binding IPI 20093360
GO:0005109 frizzled binding IEA,IBA --
GO:0005515 protein binding IPI 19072540
GO:0019904 protein domain specific binding IEA --
genes like me logo Genes that share ontologies with WNT3A: view
genes like me logo Genes that share phenotypes with WNT3A: view

Human Phenotype Ontology for WNT3A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for WNT3A Gene

MGI Knock Outs for WNT3A:

Animal Model Products

  • Taconic Biosciences Mouse Models for WNT3A

Clone Products

  • Addgene plasmids for WNT3A

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for WNT3A Gene

Localization for WNT3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for WNT3A 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 WNT3A gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 5
golgi apparatus 5
endosome 4
cytoskeleton 2
nucleus 2
mitochondrion 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for WNT3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA,ISS --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005796 Golgi lumen TAS --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with WNT3A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for WNT3A Gene

Pathways & Interactions for WNT3A Gene

genes like me logo Genes that share pathways with WNT3A: view

Pathways by source for WNT3A Gene

SIGNOR curated interactions for WNT3A Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for WNT3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001649 osteoblast differentiation IEA --
GO:0001701 in utero embryonic development IEA --
GO:0001756 somitogenesis IEA --
GO:0001819 positive regulation of cytokine production IEA --
GO:0001934 positive regulation of protein phosphorylation IDA,IEA 20137080
genes like me logo Genes that share ontologies with WNT3A: view

Drugs & Compounds for WNT3A Gene

(1) Drugs for WNT3A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for WNT3A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with WNT3A: view

Transcripts for WNT3A Gene

mRNA/cDNA for WNT3A Gene

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

Unigene Clusters for WNT3A Gene

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

Clone Products

  • Addgene plasmids for WNT3A

Alternative Splicing Database (ASD) splice patterns (SP) for WNT3A Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b

Relevant External Links for WNT3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for WNT3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for WNT3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for WNT3A Gene

This gene is overexpressed in Lung (x14.1), Skin - Sun Exposed (Lower leg) (x7.3), Skin - Not Sun Exposed (Suprapubic) (x7.1), Prostate (x4.7), and Esophagus - Mucosa (x4.4).

Protein differential expression in normal tissues from HIPED for WNT3A Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for WNT3A Gene

Protein tissue co-expression partners for WNT3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of WNT3A Gene:


SOURCE GeneReport for Unigene cluster for WNT3A Gene:


mRNA Expression by UniProt/SwissProt for WNT3A Gene:

Tissue specificity: Moderately expressed in placenta and at low levels in adult lung, spleen, and prostate.

Evidence on tissue expression from TISSUES for WNT3A Gene

  • Nervous system(2.7)
  • Blood(2.6)
  • Bone marrow(2.6)
  • Intestine(2.5)
  • Muscle(2.5)
  • Skin(2.5)
  • Heart(2.4)
  • Liver(2.4)
  • Bone(2.3)
  • Kidney(2.3)
  • Lung(2.3)
  • Eye(2.1)
  • Pancreas(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for WNT3A Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • skeleton
Head and neck:
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with WNT3A: view

Orthologs for WNT3A Gene

This gene was present in the common ancestor of animals.

Orthologs for WNT3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia WNT3A 34 33
  • 99.34 (n)
(Canis familiaris)
Mammalia WNT3A 34 33
  • 91.57 (n)
(Ornithorhynchus anatinus)
Mammalia WNT3A 34
  • 90 (a)
(Monodelphis domestica)
Mammalia WNT3A 34
  • 90 (a)
(Bos Taurus)
Mammalia WNT3A 34 33
  • 89 (n)
(Mus musculus)
Mammalia Wnt3a 16 34 33
  • 87.5 (n)
(Rattus norvegicus)
Mammalia Wnt3a 33
  • 85.6 (n)
(Gallus gallus)
Aves WNT3A 34 33
  • 78.69 (n)
(Anolis carolinensis)
Reptilia WNT3A 34
  • 89 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia wnt3a 33
  • 73.96 (n)
(Danio rerio)
Actinopterygii wnt3a 34 33
  • 78.5 (n)
fruit fly
(Drosophila melanogaster)
Insecta Wnt2 35
  • 46 (a)
Wnt6 35
  • 45 (a)
Wnt5 35
  • 42 (a)
Wnt4 35
  • 32 (a)
(Caenorhabditis elegans)
Secernentea cwn-2 35
  • 40 (a)
cwn-1 34 35
  • 37 (a)
egl-20 35
  • 36 (a)
mom-2 35
  • 31 (a)
lin-44 35
  • 31 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
Species where no ortholog for WNT3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 WNT3A Gene

Gene Tree for WNT3A (if available)
Gene Tree for WNT3A (if available)
Evolutionary constrained regions (ECRs) for WNT3A: view image

Paralogs for WNT3A Gene

Paralogs for WNT3A Gene

(17) SIMAP similar genes for WNT3A Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with WNT3A: view

Variants for WNT3A Gene

Sequence variations from dbSNP and Humsavar for WNT3A Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000026843 -- 228,013,599(+) A/T intron_variant
rs1000066759 -- 228,008,914(+) A/G intron_variant
rs1000182727 -- 228,030,844(+) T/C intron_variant
rs1000276301 -- 228,019,133(+) A/T intron_variant
rs1000366662 -- 228,059,833(+) T/C 3_prime_UTR_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for WNT3A Gene

Variant ID Type Subtype PubMed ID
dgv79e214 CNV loss 21293372
esv32853 CNV gain 17666407
esv3589043 CNV gain 21293372
nsv1075807 CNV duplication 25765185
nsv516409 CNV loss 19592680
nsv523935 CNV loss 19592680
nsv826908 CNV gain 20364138
nsv826953 CNV gain 20364138
nsv826964 CNV gain 20364138
nsv832803 CNV loss 17160897
nsv952134 CNV deletion 24416366

Variation tolerance for WNT3A Gene

Residual Variation Intolerance Score: 20.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.65; 13.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for WNT3A 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 WNT3A Gene

Disorders for WNT3A Gene

MalaCards: The human disease database

(8) MalaCards diseases for WNT3A Gene - From: HGMD, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
osteoporosis, juvenile
  • idiopathic juvenile osteoporosis; ijo
diarrhea 4, malabsorptive, congenital
  • diar4
craniodiaphyseal dysplasia
  • cdd
focal dermal hypoplasia
  • fdh
chemical colitis
- elite association - COSMIC cancer census association via MalaCards
Search WNT3A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for WNT3A

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 WNT3A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for WNT3A Gene

Publications for WNT3A Gene

  1. Molecular cloning and characterization of WNT3A and WNT14 clustered in human chromosome 1q42 region. (PMID: 11414706) Saitoh T … Katoh M (Biochemical and biophysical research communications 2001) 2 3 4 22 58
  2. Active and water-soluble form of lipidated Wnt protein is maintained by a serum glycoprotein afamin/α-albumin. (PMID: 26902720) Mihara E … Takagi J (eLife 2016) 3 4 58
  3. Disulfide bond requirements for active Wnt ligands. (PMID: 24841207) MacDonald BT … He X (The Journal of biological chemistry 2014) 3 4 58
  4. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 44 58
  5. Wingless (Wnt)-3A induces trophoblast migration and matrix metalloproteinase-2 secretion through canonical Wnt signaling and protein kinase B/AKT activation. (PMID: 19887570) Sonderegger S … Knöfler M (Endocrinology 2010) 3 22 58

Products for WNT3A Gene

Sources for WNT3A Gene

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