WNT3 (Wnt family member 3)

Gene

• Entrez ID: 7473
• Gene name: Wnt family member 3
• Gene symbol: WNT3
• Synonyms: 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:0005109	Function	Frizzled binding	IBA	21873635
GO:0005109	Function	Frizzled binding	IPI	10557084, 18313787
GO:0005125	Function	Cytokine activity	IBA	21873635
GO:0005515	Function	Protein binding	IPI	18313787, 21314951, 26902720
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA	21873635
GO:0005615	Component	Extracellular space	TAS	18313787
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:0009948	Process	Anterior/posterior axis specification	IEA
GO:0009950	Process	Dorsal/ventral axis specification	IEA
GO:0010628	Process	Positive regulation of gene expression	IDA	25640183
GO:0016055	Process	Wnt signaling pathway	TAS
GO:0019904	Function	Protein domain specific binding	IEA
GO:0030177	Process	Positive regulation of Wnt signaling pathway	IEA
GO:0030182	Process	Neuron differentiation	IBA	21873635
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:0044338	Process	Canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation	IMP	20039315
GO:0044339	Process	Canonical Wnt signaling pathway involved in osteoblast differentiation	IMP	20039315
GO:0045165	Process	Cell fate commitment	IBA	21873635
GO:0048018	Function	Receptor ligand activity	IC	18044981
GO:0048018	Function	Receptor ligand activity	IDA	10557084, 28733458
GO:0048697	Process	Positive regulation of collateral sprouting in absence of injury	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	21873635
GO:0060070	Process	Canonical Wnt signaling pathway	IDA	10557084, 15588944, 18044981, 28733458
GO:0060070	Process	Canonical Wnt signaling pathway	TAS	24115276
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:1904954	Process	Canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation	IMP	25640183
GO:1905474	Process	Canonical Wnt signaling pathway involved in stem cell proliferation	IDA	25640183
GO:1990909	Component	Wnt signalosome	IC	10557084
GO:1990909	Component	Wnt signalosome	NAS	24115276

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
Disease name	Disease term	dbSNP ID	References
Agenesis of corpus callosum	Agenesis of corpus callosum	rs754914260, rs1057519053, rs1057519056, rs1057519054, rs1057519055, rs1057519057, rs1384496494, rs1599017933
Atrial fibrillation	Atrial Fibrillation	rs120074192, rs121908590, rs121908593, rs121434558, rs587776851, rs387906612, rs387906613, rs387906614, rs387906615, rs199472687, rs199472705, rs199473324, rs587777336, rs587777339, rs587777557, rs587777558, rs587777559, rs587777560, rs886037778, rs769405762, rs770372675	30061737
Bladder exstrophy and epispadias complex	Bladder Exstrophy and Epispadias Complex	rs786205887
Breast carcinoma	Breast Carcinoma	rs80359671, rs11540652, rs28934575, rs28897672, rs137886232, rs193922376, rs80357783, rs80359306, rs80359405, rs80359507, rs80359598, rs80358429, rs397507683, rs397515636, rs80359451, rs397507859, rs80359709, rs80359742, rs80359205, rs80357627, rs80357004, rs80357571, rs80357767, rs80357653, rs80358086, rs80357608, rs28897696, rs41293465, rs146650273, rs63751017, rs63750617, rs63750726, rs63750199, rs63749848, rs398122618, rs398122653, rs397509211, rs80357791, rs121912666, rs587778541, rs121908698, rs536907995, rs587781302, rs140342925, rs587781506, rs587782652, rs587782849, rs587783057, rs10520699, rs11852999, rs139770721, rs374950566, rs786202800, rs863224451, rs377153250, rs747727055, rs876658804, rs780001540, rs760815829, rs878854926, rs775248597, rs886040658, rs886040192, rs786203523, rs886040319, rs397508006, rs587782011, rs1060502772, rs1555461727, rs1553333072, rs1114167702, rs1257401983, rs886040950, rs1060502759, rs774684620, rs142947311, rs1555580883, rs748513310, rs376170600, rs863224499, rs1593909229, rs748453607, rs1294578913, rs1574737047, rs1593909960, rs2081922847, rs2082559544, rs2053694038	29059683
Cataract	Cataract	rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322, rs121917775, rs121917735, rs121917736, rs137853199, rs137853200, rs121917867, rs121917869, rs121913555, rs104893736, rs121909595, rs121909596, rs121909597, rs28931605, rs121909598, rs104893618, rs1695062782, rs74315486, rs74315487, rs74315490, rs74315489, rs745938679, rs1566402656, rs74315439, rs74315441, rs121912973, rs121917823, rs1593332981, rs121917825, rs121917827, rs113994108, rs387906963, rs387906964, rs1240503246, rs387906965, rs387906966, rs750207077, rs387907336, rs387907337, rs387907342, rs140332366, rs397514703, rs398122937, rs398122378, rs398122392, rs398122944, rs137853924, rs398122947, rs397515623, rs397515624, rs397515625, rs397515626, rs398122948, rs587778872, rs398123066, rs587777601, rs370424081, rs786205221, rs786205222, rs864309684, rs864309688, rs864309701, rs864309689, rs864309690, rs864309681, rs864309686, rs864309696, rs864309693, rs864309687, rs864309691, rs864309692, rs864309695, rs864309678, rs864309685, rs864309700, rs864309698, rs864309683, rs864309682, rs864309679, rs111534978, rs864309680, rs864309702, rs864622780, rs756898971, rs869312732, rs775038545, rs878852983, rs1114167312, rs1114167313, rs1114167314, rs1114167315, rs1114167307, rs886041410, rs886041412, rs1057518738, rs1057517926, rs1057518878, rs1057519616, rs12799308, rs1064793935, rs1064797219, rs1085307126, rs1085307127, rs765628635, rs1114167427, rs1114167433, rs1554744860, rs1554743428, rs747093432, rs1411557416, rs1555179713, rs1481963503, rs1555549755, rs1456161420, rs1555547008, rs1555889308, rs1555888762, rs766522434, rs1264025914, rs1553585262, rs1567671947, rs1337897299, rs764945940, rs1307969607, rs949335475, rs1184095219, rs776129797, rs1569203234, rs1567668570, rs749141857, rs764098604, rs1184398243, rs1578956689, rs1568480054, rs1564745688, rs1564722302, rs1564723150, rs1571175950, rs1569602837, rs1576552712, rs1575369255, rs981126461, rs1570403798, rs200557771, rs1477743112, rs1651879427, rs1651881222, rs1651919374, rs2024441691, rs148284531, rs1246080692
Cryptorchidism	Cryptorchidism	rs121912555, rs104894697, rs104894698, rs398122886
Hydrocephalus	Hydrocephalus	rs387907320, rs369384363, rs387907321, rs372127610, rs770273135, rs797045095, rs797045707, rs769795916, rs781251438, rs922703465, rs376078512, rs1567043467, rs1587149916, rs1586841546
Microphthalmos	Microphthalmos	rs794726862, rs1329285216
Optic atrophy	Optic Atrophy	rs121434508, rs267607017, rs80356524, rs80356525, rs879255560, rs104893753, rs80356529, rs397515360, rs104893620, rs199476104, rs199476112, rs199476118, rs398124298, rs770066665, rs398124299, rs61750185, rs672601379, rs727504060, rs786204830, rs794727804, rs199946797, rs863224127, rs863224131, rs863224134, rs863224906, rs372054380, rs886037828, rs764791523, rs145639028, rs1057519312, rs1064794257, rs1064794656, rs1064797303, rs774265764, rs760337383, rs1553784985, rs72653786, rs1555229948, rs1555119216, rs761743852, rs1553785338, rs1020764190, rs782581701, rs1560408865, rs761460379, rs773022324, rs782740998, rs1560327427, rs80356528, rs1734162973, rs1716524583, rs1057368575
Parkinson disease	Parkinson Disease	rs116074753, rs118203903, rs118203904, rs115735611, rs33939927, rs35801418, rs34805604, rs35870237, rs34995376, rs74315355, rs28940284, rs74315356, rs74315357, rs28940285, rs730880302, rs750664040, rs74315359, rs74315360, rs45539432, rs74315361, rs119451946, rs80356771, rs74500255, rs75822236, rs1141814, rs78973108, rs121908681, rs121908686, rs121908687, rs137853054, rs137853055, rs137853056, rs137853057, rs137853058, rs137853059, rs34424986, rs137853060, rs397518439, rs28938172, rs74315351, rs74315353, rs137853051, rs118192098, rs121917767, rs121918104, rs1589451049, rs104893877, rs104893878, rs283413, rs112176450, rs111290936, rs188286943, rs387906863, rs387906864, rs774631197, rs199935023, rs387906942, rs397514694, rs398122403, rs398122404, rs398122405, rs104886460, rs409652, rs431905511, rs63751392, rs756677845, rs864309527, rs864309650, rs750014782, rs1554391082, rs864622011, rs869312810, rs869312809, rs869312811, rs369100678, rs879253853, rs869320761, rs747506979, rs879255630, rs886039854, rs191486604, rs781442277, rs1060499619, rs751037529, rs55777503, rs768091663, rs34208370, rs1553122929, rs772786691, rs754809877, rs1555907463, rs1557561340, rs781600849, rs141263564, rs1557901552, rs777160388, rs756783990, rs867929413, rs1237637353, rs1005937012, rs755000580, rs747427602, rs1578089802, rs771586218, rs748142049, rs1582953433, rs746646126, rs771529549, rs121918106	24511991, 21812969, 22451204, 21738487
Tetraamelia syndrome	Tetraamelia multiple malformations, TETRAAMELIA SYNDROME, AUTOSOMAL RECESSIVE	rs104894653, rs1554579568, rs1554576888	14872406

Unknown
Disease name	Disease term	dbSNP ID	References
Atresia of vagina	Atresia of vagina
Celiac disease	Celiac Disease	rs2305764, rs35218876	20190752
Choanal atresia	Choanal Atresia
Adrenal gland agenesis	Congenital absence of adrenal gland
Asplenia	Congenital absence of spleen
Congenital coloboma of iris	Congenital coloboma of iris
Pulmonary hypoplasia	Congenital hypoplasia of lung	rs1569032634
Gastroschisis	Gastroschisis
Imperforate anus	Anus, Imperforate
Lung diseases	Lung Diseases, Interstitial		23583980
Malignant lymphoma, lymphocytic, intermediate differentiation	Malignant lymphoma, lymphocytic, intermediate differentiation, diffuse		18787224
Lymphoma, lymphocytic, intermediate	Lymphoma, Lymphocytic, Intermediate		18787224
Malignant mesothelioma	Malignant mesothelioma		25756049
Mental depression	Major Depressive Disorder	rs587778876, rs587778877	29942085
Microcornea	Microcornea
Micrognathism	Micrognathism
Microstomia	Microstomia
Microtia	Congenital small ears
Mood disorder	Mood Disorders		29942085
Multicystic renal dysplasia	Multicystic Dysplastic Kidney
Oral cleft	Oral cleft
Paroxysmal atrial fibrillation	Paroxysmal atrial fibrillation	rs199865688, rs397515994, rs757096307	30061737
Biliary cirrhosis	Primary biliary cirrhosis		22961000
Renal agenesis	Congenital absence of kidneys syndrome
Septo-optic dysplasia	Septo-Optic Dysplasia
Tetraamelia	Tetra-amelia autosomal recessive, Tetraamelia-multiple malformations syndrome		14872406, 18837045
Tracheal stenosis	Tracheal Stenosis
Urethral atresia	Urethral atresia