WNT3 (Wnt family member 3)

Gene

• Entrez ID: 7473
• Gene name: Wnt family member 3
• Gene symbol: WNT3
• Synonyms (NCBI Gene): INT4, TETAMS
• Chromosome: 17
• Chromosome location: 17q21.31-q21.32
• 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 embryog

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018503	hsa-miR-335-5p	Microarray	18185580
MIRT024672	hsa-miR-215-5p	Microarray	19074876
MIRT026683	hsa-miR-192-5p	Microarray	19074876
MIRT036062	hsa-miR-1301-3p	CLASH	23622248
MIRT696724	hsa-miR-1255b-2-3p	HITS-CLIP	23313552
MIRT696723	hsa-miR-5684	HITS-CLIP	23313552
MIRT696722	hsa-miR-3667-3p	HITS-CLIP	23313552
MIRT696721	hsa-miR-659-5p	HITS-CLIP	23313552
MIRT696720	hsa-miR-155-3p	HITS-CLIP	23313552
MIRT696719	hsa-miR-3685	HITS-CLIP	23313552
MIRT463929	hsa-miR-1321	PAR-CLIP	23592263
MIRT463928	hsa-miR-4739	PAR-CLIP	23592263
MIRT463927	hsa-miR-4756-5p	PAR-CLIP	23592263
MIRT463926	hsa-miR-125a-3p	PAR-CLIP	23592263
MIRT463925	hsa-miR-4487	PAR-CLIP	23592263
MIRT463924	hsa-miR-3126-5p	PAR-CLIP	23592263
MIRT463923	hsa-miR-6875-5p	PAR-CLIP	23592263
MIRT463922	hsa-miR-4419a	PAR-CLIP	23592263
MIRT463921	hsa-miR-4510	PAR-CLIP	23592263
MIRT463920	hsa-miR-6127	PAR-CLIP	23592263
MIRT463919	hsa-miR-6129	PAR-CLIP	23592263
MIRT463918	hsa-miR-6130	PAR-CLIP	23592263
MIRT463917	hsa-miR-6133	PAR-CLIP	23592263
MIRT463915	hsa-miR-3665	PAR-CLIP	23592263
MIRT463916	hsa-miR-4731-5p	PAR-CLIP	23592263
MIRT463914	hsa-miR-6077	PAR-CLIP	23592263
MIRT463913	hsa-miR-766-5p	PAR-CLIP	23592263
MIRT463912	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT463911	hsa-miR-4710	PAR-CLIP	23592263
MIRT463910	hsa-miR-6834-5p	PAR-CLIP	23592263
MIRT735183	hsa-miR-206	Immunohistochemistry (IHC), qRT-PCR, In situ hybridization	32722078
MIRT696724	hsa-miR-1255b-2-3p	HITS-CLIP	23313552
MIRT696723	hsa-miR-5684	HITS-CLIP	23313552
MIRT696722	hsa-miR-3667-3p	HITS-CLIP	23313552
MIRT696721	hsa-miR-659-5p	HITS-CLIP	23313552
MIRT696720	hsa-miR-155-3p	HITS-CLIP	23313552
MIRT696719	hsa-miR-3685	HITS-CLIP	23313552
MIRT463929	hsa-miR-1321	PAR-CLIP	23592263
MIRT463928	hsa-miR-4739	PAR-CLIP	23592263
MIRT463927	hsa-miR-4756-5p	PAR-CLIP	23592263
MIRT463926	hsa-miR-125a-3p	PAR-CLIP	23592263
MIRT463925	hsa-miR-4487	PAR-CLIP	23592263
MIRT463924	hsa-miR-3126-5p	PAR-CLIP	23592263
MIRT463923	hsa-miR-6875-5p	PAR-CLIP	23592263
MIRT463922	hsa-miR-4419a	PAR-CLIP	23592263
MIRT463921	hsa-miR-4510	PAR-CLIP	23592263
MIRT463920	hsa-miR-6127	PAR-CLIP	23592263
MIRT463919	hsa-miR-6129	PAR-CLIP	23592263
MIRT463918	hsa-miR-6130	PAR-CLIP	23592263
MIRT463917	hsa-miR-6133	PAR-CLIP	23592263
MIRT463915	hsa-miR-3665	PAR-CLIP	23592263
MIRT463916	hsa-miR-4731-5p	PAR-CLIP	23592263
MIRT463914	hsa-miR-6077	PAR-CLIP	23592263
MIRT463913	hsa-miR-766-5p	PAR-CLIP	23592263
MIRT463912	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT463911	hsa-miR-4710	PAR-CLIP	23592263
MIRT463910	hsa-miR-6834-5p	PAR-CLIP	23592263
MIRT756009	hsa-miR-3198	Luciferase reporter assay, Western blotting, qRT-PCR	38536597

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000902	Process	Cell morphogenesis	IMP	15588944
GO:0001707	Process	Mesoderm formation	IEA
GO:0005102	Function	Signaling receptor binding	IEA
GO:0005109	Function	Frizzled binding	IBA
GO:0005109	Function	Frizzled binding	IPI	10557084, 18313787
GO:0005125	Function	Cytokine activity	IBA
GO:0005515	Function	Protein binding	IPI	18313787, 21314951, 26902720, 31036956
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA
GO:0005615	Component	Extracellular space	IEA
GO:0005615	Component	Extracellular space	TAS	18313787
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005796	Component	Golgi lumen	TAS
GO:0005886	Component	Plasma membrane	TAS
GO:0007276	Process	Gamete generation	IEA
GO:0007411	Process	Axon guidance	IEA
GO:0009653	Process	Anatomical structure morphogenesis	IEA
GO:0009948	Process	Anterior/posterior axis specification	IEA
GO:0009950	Process	Dorsal/ventral axis specification	IEA
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0010467	Process	Gene expression	IEA
GO:0010628	Process	Positive regulation of gene expression	IDA	25640183
GO:0010628	Process	Positive regulation of gene expression	IEA
GO:0010628	Process	Positive regulation of gene expression	IEA
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0019904	Function	Protein domain specific binding	IEA
GO:0030177	Process	Positive regulation of Wnt signaling pathway	IEA
GO:0030182	Process	Neuron differentiation	IBA
GO:0030182	Process	Neuron differentiation	ISS
GO:0030666	Component	Endocytic vesicle membrane	TAS
GO:0031012	Component	Extracellular matrix	IEA
GO:0035115	Process	Embryonic forelimb morphogenesis	IEA
GO:0035116	Process	Embryonic hindlimb morphogenesis	IEA
GO:0045165	Process	Cell fate commitment	IBA
GO:0045597	Process	Positive regulation of cell differentiation	IEA
GO:0045669	Process	Positive regulation of osteoblast differentiation	IMP	20039315
GO:0048018	Function	Receptor ligand activity	IC	18044981
GO:0048018	Function	Receptor ligand activity	IDA	10557084, 28733458
GO:0048513	Process	Animal organ development	IEA
GO:0048646	Process	Anatomical structure formation involved in morphogenesis	IEA
GO:0048697	Process	Positive regulation of collateral sprouting in absence of injury	IEA
GO:0048731	Process	System development	IEA
GO:0048843	Process	Negative regulation of axon extension involved in axon guidance	IEA
GO:0050767	Process	Regulation of neurogenesis	IMP	25640183
GO:0060064	Process	Spemann organizer formation at the anterior end of the primitive streak	IEA
GO:0060070	Process	Canonical Wnt signaling pathway	IBA
GO:0060070	Process	Canonical Wnt signaling pathway	IDA	10557084, 15588944, 18044981, 25640183, 28733458
GO:0060070	Process	Canonical Wnt signaling pathway	IEA
GO:0060070	Process	Canonical Wnt signaling pathway	IEA
GO:0060070	Process	Canonical Wnt signaling pathway	IMP	20039315
GO:0060070	Process	Canonical Wnt signaling pathway	TAS	24115276
GO:0060173	Process	Limb development	IEA
GO:0060173	Process	Limb development	IEA
GO:0060174	Process	Limb bud formation	IMP	14872406
GO:0060323	Process	Head morphogenesis	IEA
GO:0061180	Process	Mammary gland epithelium development	IEP	8168088
GO:0070062	Component	Extracellular exosome	TAS
GO:0071300	Process	Cellular response to retinoic acid	ISS
GO:0072089	Process	Stem cell proliferation	IMP	25640183
GO:0098588	Component	Bounding membrane of organelle	IEA
GO:1904948	Process	Midbrain dopaminergic neuron differentiation	IMP	25640183
GO:1990909	Component	Wnt signalosome	IC	10557084
GO:1990909	Component	Wnt signalosome	NAS	24115276
GO:2000739	Process	Regulation of mesenchymal stem cell differentiation	IMP	20039315

Other IDs

• MIM: 165330
• HGNC: 12782
• e!Ensembl: ENSG00000108379

Protein

• UniProt ID: P56703
• Protein name: Proto-oncogene Wnt-3 (Proto-oncogene Int-4 homolog)
• Protein 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 nor
• PDB: 6AHY
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00110	wnt	47 → 355	wnt family	Family

• Sequence:

  MEPHLLGLLLGLLLGGTRVLAGYPIWWSLALGQQYTSLGSQPLLCGSIPGLVPKQLRFCR
  NYIEIMPSVAEGVKLGIQECQHQFRGRRWNCTTIDDSLAIFGPVLDKATRESAFVHAIAS
  AGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRP
  DARSAMNKHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDFLKDKYDS
  ASEMVVEKHRESRGWVETLRAKYSLFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTC
  NVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRIYDVHTCK

• Sequence length: 355

Pathways

KEGG:

mTOR signaling pathway
Wnt signaling pathway
Hippo signaling pathway
Signaling pathways regulating pluripotency of stem cells
Melanogenesis
Cushing syndrome
Alzheimer disease
Pathways of neurodegeneration - multiple diseases
Human papillomavirus infection
Pathways in cancer
Proteoglycans in cancer
MicroRNAs in cancer
Basal cell carcinoma
Breast cancer
Hepatocellular carcinoma
Gastric cancer

Reactome:

TCF dependent signaling in response to WNT
WNT ligand biogenesis and trafficking

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Bladder exstrophy-epispadias-cloacal extrophy complex	Likely pathogenic	rs786205887	RCV000172899
Tetraamelia syndrome 1	Pathogenic	rs104894653	RCV000014823

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
WNT3-related disorder	Likely benign; Benign	rs150717986, rs143605657, rs767605103	RCV003971108 RCV003958862 RCV004758926

Associations from Text Mining
Disease Name	Relationship Type	References
Acute Radiation Syndrome	Associate	33476246, 35680903, 37676284, 38499035
Alzheimer Disease	Associate	31504236, 36191742
Amyotrophic Lateral Sclerosis	Stimulate	30924074
Aortic Valve Stenosis	Associate	29227539
Autism Spectrum Disorder	Associate	37907504
Bladder Exstrophy	Associate	34355505
Breast Neoplasms	Associate	23071104, 30651373
Carcinogenesis	Associate	17767013, 29565490
Carcinoma Hepatocellular	Associate	18313787, 18577996, 36275697
Carcinoma Non Small Cell Lung	Stimulate	29565490
Celiac Disease	Associate	35208504
Cleft Lip	Associate	20890934
Cleft Palate	Associate	26505415
Cognition Disorders	Associate	37286376
Colorectal Neoplasms	Associate	33331430, 33891491
COVID 19	Associate	34183789, 37286376
Crohn Disease	Associate	26512113
Drug Hypersensitivity	Associate	37864206
Endometrial Neoplasms	Inhibit	9099960
Esophageal Squamous Cell Carcinoma	Associate	31851619
Essential Hypertension	Associate	32392180
Gallbladder Diseases	Associate	26111189
Glioma	Associate	32181818, 34657400
Growth Disorders	Stimulate	15588944
Heart Defects Congenital	Associate	33463545
Hematologic Diseases	Associate	37676284
Heterotaxy Syndrome	Associate	26111189
Hippocampal Sclerosis	Associate	36191742
Infections	Associate	21169917
Inflammation	Stimulate	24549785
Inflammation	Associate	32271446
KBG syndrome	Associate	32030560
Klatskin Tumor	Associate	26972709
Leukemia	Associate	36595475
Leukemia Lymphocytic Chronic B Cell	Associate	14973184
Leukemia Myelogenous Chronic BCR ABL Positive	Associate	37864206
Leukemia Myeloid Acute	Associate	17767013
Leukemia Prolymphocytic T Cell	Associate	27651098
Leukoplakia Oral	Associate	17922924
Lung Neoplasms	Stimulate	29565490
Lymphoma Mantle Cell	Associate	18787224, 34633777
Mental Disorders	Associate	31504236
Neoplasm Metastasis	Inhibit	30651373
Neoplasms	Stimulate	18313787
Neoplasms	Associate	18577996
Neoplasms	Inhibit	24549785
Orofacial Cleft 1	Associate	26505415
Osteoarthritis	Associate	31155960
Otofaciocervical Syndrome	Associate	35191549
Parkinson Disease	Associate	21812969, 28586827, 31504236
Periapical Periodontitis	Associate	31831777
Polycystic Ovary Syndrome	Associate	29510649
Precancerous Conditions	Associate	34275925
Retinal Dysplasia	Associate	17922924
Schizophrenia	Associate	31504236
Stomach Neoplasms	Stimulate	34275925
Triple Negative Breast Neoplasms	Associate	21152100
Tuberculosis Pulmonary	Associate	21169917
Uniparental Disomy	Associate	21152100