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... See more...

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 4
  • WNT3A 5

External Ids for WNT3A Gene

Previous GeneCards Identifiers for WNT3A Gene

  • GC01P226691
  • GC01P223933
  • GC01P224580
  • GC01P225169
  • GC01P224501
  • GC01P226261
  • GC01P228194
  • GC01P198726
  • GC01P228007
  • GC01P228013
  • GC01P228017
  • GC01P228072

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 Hypotrichosis Simplex. Among its related pathways are Gene regulatory network modelling somitogenesis and Signaling by GPCR. 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 Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for WNT3A Gene

Genomics for WNT3A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for WNT3A Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for WNT3A

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

Genomic Locations for WNT3A Gene

Genomic Locations for WNT3A Gene
chr1:228,006,998-228,067,113
(GRCh38/hg38)
Size:
60,116 bases
Orientation:
Plus strand
chr1:228,194,723-228,248,972
(GRCh37/hg19)
Size:
54,250 bases
Orientation:
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:
    P56704-WNT3A_HUMAN
    Recommended name:
    Protein Wnt-3a
    Protein Accession:
    P56704
    Secondary Accessions:
    • Q3SY79
    • Q3SY80
    • Q969P2

    Protein attributes for WNT3A Gene

    Size:
    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). Interacts with glypican GPC3 (PubMed:16227623). Interacts with PKD1 (via extracellular domain) (PubMed:27214281).

    Alternative splice isoforms for WNT3A Gene

    UniProtKB/Swiss-Prot:

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 Asn87 and Asn298
  • Modification sites at PhosphoSitePlus

Other Protein References for WNT3A Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for WNT3A

No data available for DME Specific Peptides for WNT3A Gene

Domains & Families for WNT3A Gene

Gene Families for WNT3A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for WNT3A Gene

InterPro:
Blocks:
  • Secreted growth factor Wnt protein
ProtoNet:

Suggested Antigen Peptide Sequences for WNT3A Gene

GenScript: Design optimal peptide antigens:
  • Protein Wnt (Q3SY79_HUMAN)
  • Protein Wnt-3a (WNT3A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P56704

UniProtKB/Swiss-Prot:

WNT3A_HUMAN :
  • Belongs to the Wnt family.
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).

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 IEA --
GO:0005102 signaling receptor binding IPI 20093360
GO:0005109 frizzled binding IEA,IBA 21873635
GO:0005125 cytokine activity IBA 21873635
GO:0005515 protein binding IPI 19072540
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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

COMPARTMENTS
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 4
endosome 4
golgi apparatus 4
cytoskeleton 3
nucleus 3
mitochondrion 2
cytosol 2
lysosome 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

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

Pathways & Interactions for WNT3A Gene

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

Pathways by source for WNT3A Gene

2 Sino Biological pathways for WNT3A Gene
2 GeneGo (Thomson Reuters) pathways for WNT3A Gene
  • Transcription Androgen Receptor nuclear signaling
  • Translation Non-genomic (rapid) action of Androgen Receptor
1 Tocris pathway for WNT3A Gene
8 Qiagen pathways for WNT3A Gene
  • Colorectal Cancer Metastasis
  • Factors Promoting Cardiogenesis in Vertebrates
  • GSK3 Signaling
  • Hedgehog Signaling in Mammals
  • Human Embryonic Stem Cell Pluripotency
1 Cell Signaling Technology pathway for WNT3A Gene
2 GeneTex pathways for WNT3A Gene

SIGNOR curated interactions for WNT3A Gene

Activates:
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 IEA,IDA 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

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for WNT3A

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP1:
SP2:

Relevant External Links for WNT3A Gene

GeneLoc Exon Structure for
WNT3A

Expression for WNT3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for WNT3A

SOURCE GeneReport for Unigene cluster for WNT3A Gene:

Hs.336930

mRNA Expression by UniProt/SwissProt for WNT3A Gene:

P56704-WNT3A_HUMAN
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(3.3)
  • Intestine(3.3)
  • Skin(3.3)
  • Blood(3.2)
  • Kidney(3.2)
  • Muscle(3.2)
  • Liver(3.1)
  • Heart(3.1)
  • Bone marrow(3.1)
  • Lung(3)
  • Pancreas(2.9)
  • Eye(2.8)
  • Bone(2.8)
  • Lymph node(2.8)
  • Thyroid gland(2.6)
  • Spleen(2.5)
  • Adrenal gland(2.5)
  • Stomach(2.1)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • skeleton
Regions:
Head and neck:
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • 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
General:
  • 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
Chimpanzee
(Pan troglodytes)
Mammalia WNT3A 30 31
  • 99.34 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia WNT3A 30 31
  • 91.57 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia WNT3A 31
  • 90 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia WNT3A 31
  • 90 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia WNT3A 30 31
  • 89 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Wnt3a 30 17 31
  • 87.5 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Wnt3a 30
  • 85.6 (n)
Chicken
(Gallus gallus)
Aves WNT3A 30 31
  • 78.69 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia WNT3A 31
  • 89 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia wnt3a 30
  • 73.96 (n)
Zebrafish
(Danio rerio)
Actinopterygii wnt3a 30 31
  • 78.5 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Wnt2 32
  • 46 (a)
Wnt6 32
  • 45 (a)
Wnt5 32
  • 42 (a)
Wnt4 32
  • 32 (a)
Worm
(Caenorhabditis elegans)
Secernentea cwn-2 32
  • 40 (a)
cwn-1 31 32
  • 37 (a)
OneToMany
egl-20 32
  • 36 (a)
lin-44 32
  • 31 (a)
mom-2 32
  • 31 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 46 (a)
OneToMany
Species where no ortholog for WNT3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

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

Paralogs for WNT3A Gene

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

  • WNT3A_HUMAN
genes like me logo Genes that share paralogs with WNT3A: view

Variants for WNT3A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for WNT3A Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
709037 Benign: not provided 228,050,742(+) G/A MISSENSE_VARIANT
722283 Benign: not provided 228,059,342(+) C/T SYNONYMOUS_VARIANT
724754 Likely Benign: not provided 228,050,906(+) C/T SYNONYMOUS_VARIANT
752476 Likely Benign: not provided 228,059,258(+) C/T SYNONYMOUS_VARIANT
755824 Benign: not provided 228,050,855(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for WNT3A Gene

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)
WNT3A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
WNT3A

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

(21) MalaCards diseases for WNT3A Gene - From: Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
osteoporosis, juvenile
  • idiopathic juvenile osteoporosis; ijo
hypotrichosis simplex
  • hhs
osteoporosis-pseudoglioma syndrome
  • oppg
colorectal cancer
  • crc
hypotrichosis
- 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 23
  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
  3. Disulfide bond requirements for active Wnt ligands. (PMID: 24841207) MacDonald BT … He X (The Journal of biological chemistry 2014) 3 4
  4. Reconstitution of a frizzled8.Wnt3a.LRP6 signaling complex reveals multiple Wnt and Dkk1 binding sites on LRP6. (PMID: 20093360) Bourhis E … Hannoush RN (The Journal of biological chemistry 2010) 3 4
  5. 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 41

Products for WNT3A Gene

  • Addgene plasmids for WNT3A

Sources for WNT3A Gene