Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	80326
Gene name	Wnt family member 10A
Gene symbol	WNT10A
Synonyms (NCBI Gene)	ECTD16OODDSSPSSTHAG4
Chromosome	2
Chromosome location	2q35
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

Show/Hide all (26)

SNP ID	Visualize variation	Clinical significance	Consequence
rs34972707	A>C	Likely-benign, pathogenic, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs77583146	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, intron variant, missense variant
rs116998555	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Intron variant, coding sequence variant, missense variant
rs121908118	G>A,T	Pathogenic	Intron variant, stop gained, coding sequence variant, missense variant
rs121908120	T>A	Conflicting-interpretations-of-pathogenicity, benign, pathogenic, likely-benign	Intron variant, coding sequence variant, missense variant
rs121908121	G>A	Likely-pathogenic, not-provided, pathogenic	Intron variant, coding sequence variant, missense variant
rs121908122	C>A	Pathogenic	Stop gained, coding sequence variant, missense variant
rs146902156	G>A	Likely-benign, not-provided, pathogenic	Missense variant, coding sequence variant, intron variant
rs147680216	G>A	Likely-benign, pathogenic, benign, uncertain-significance	Missense variant, coding sequence variant, intron variant
rs372993798	G>A,T	Pathogenic, likely-pathogenic	Intron variant, coding sequence variant, missense variant
rs750260671	G>A,T	Likely-pathogenic	Coding sequence variant, stop gained, missense variant
rs762739726	C>T	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained, intron variant
rs775380022	G>A	Likely-pathogenic	Missense variant, coding sequence variant, intron variant
rs775990266	G>-,GG	Pathogenic	Coding sequence variant, frameshift variant
rs886039453	C>T	Pathogenic	Stop gained, coding sequence variant, intron variant
rs886039454	C>G	Pathogenic	Stop gained, coding sequence variant, synonymous variant
rs886041618	->C	Pathogenic	Coding sequence variant, frameshift variant
rs1011303295	T>A,C	Pathogenic	Missense variant, coding sequence variant
rs1057520655	A>G	Pathogenic	Missense variant, coding sequence variant, intron variant
rs1060499588	C>T	Likely-pathogenic	Coding sequence variant, stop gained, intron variant
rs1085308031	G>A	Likely-pathogenic	Synonymous variant, missense variant, coding sequence variant
rs1268725013	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1553623281	AT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553623389	C>A	Pathogenic	Stop gained, coding sequence variant, missense variant
rs1575233692	C>-	Pathogenic	Frameshift variant, intron variant, coding sequence variant
rs1575235227	G>A	Pathogenic	Synonymous variant, coding sequence variant, missense variant

Show/Hide all (58)

miRTarBase ID	miRNA	Experiments	Reference
MIRT053636	hsa-miR-130a-3p	Microarray	22942087
MIRT533154	hsa-miR-4724-5p	PAR-CLIP	22012620
MIRT533153	hsa-miR-4690-3p	PAR-CLIP	22012620
MIRT533152	hsa-miR-5685	PAR-CLIP	22012620
MIRT533151	hsa-miR-361-3p	PAR-CLIP	22012620
MIRT533150	hsa-miR-4539	PAR-CLIP	22012620
MIRT533149	hsa-miR-1285-3p	PAR-CLIP	22012620
MIRT533148	hsa-miR-3187-5p	PAR-CLIP	22012620
MIRT533147	hsa-miR-5189-5p	PAR-CLIP	22012620
MIRT533146	hsa-miR-612	PAR-CLIP	22012620
MIRT533145	hsa-miR-6860	PAR-CLIP	22012620
MIRT533144	hsa-miR-4486	PAR-CLIP	22012620
MIRT533143	hsa-miR-378g	PAR-CLIP	22012620
MIRT533142	hsa-miR-3120-5p	PAR-CLIP	22012620
MIRT533141	hsa-miR-27a-5p	PAR-CLIP	22012620
MIRT533140	hsa-miR-203b-3p	PAR-CLIP	22012620
MIRT533139	hsa-miR-1231	PAR-CLIP	22012620
MIRT726098	hsa-miR-19a-3p	HITS-CLIP	22473208
MIRT726097	hsa-miR-19b-3p	HITS-CLIP	22473208
MIRT736197	hsa-miR-378a-3p	ImmunofluorescenceLuciferase reporter assayqRT-PCRWestern blot	27832641
MIRT736197	hsa-miR-378a-3p	ImmunofluorescenceLuciferase reporter assayqRT-PCRWestern blot	27832641
MIRT533151	hsa-miR-361-3p	HITS-CLIP	28735896
MIRT533153	hsa-miR-4690-3p	HITS-CLIP	28735896
MIRT533152	hsa-miR-5685	HITS-CLIP	28735896
MIRT736197	hsa-miR-378a-3p	Luciferase reporter assayWestern blottingImmunohistochemistry (IHC)qRT-PCR	32829178
MIRT533151	hsa-miR-361-3p	Luciferase reporter assayWestern blottingqRT-PCR	33299350
MIRT533154	hsa-miR-4724-5p	PAR-CLIP	22012620
MIRT533153	hsa-miR-4690-3p	PAR-CLIP	22012620
MIRT533152	hsa-miR-5685	PAR-CLIP	22012620
MIRT533151	hsa-miR-361-3p	PAR-CLIP	22012620
MIRT533150	hsa-miR-4539	PAR-CLIP	22012620
MIRT533149	hsa-miR-1285-3p	PAR-CLIP	22012620
MIRT533148	hsa-miR-3187-5p	PAR-CLIP	22012620
MIRT533147	hsa-miR-5189-5p	PAR-CLIP	22012620
MIRT533146	hsa-miR-612	PAR-CLIP	22012620
MIRT533145	hsa-miR-6860	PAR-CLIP	22012620
MIRT533144	hsa-miR-4486	PAR-CLIP	22012620
MIRT533143	hsa-miR-378g	PAR-CLIP	22012620
MIRT533142	hsa-miR-3120-5p	PAR-CLIP	22012620
MIRT533141	hsa-miR-27a-5p	PAR-CLIP	22012620
MIRT533140	hsa-miR-203b-3p	PAR-CLIP	22012620
MIRT533139	hsa-miR-1231	PAR-CLIP	22012620
MIRT755397	hsa-miR-148a-3p	Luciferase reporter assayqRT-PCR	35958896
MIRT1493547	hsa-miR-2392	CLIP-seq
MIRT1493548	hsa-miR-4494	CLIP-seq
MIRT1493549	hsa-miR-4499	CLIP-seq
MIRT1493550	hsa-miR-4513	CLIP-seq
MIRT1493551	hsa-miR-451b	CLIP-seq
MIRT1493552	hsa-miR-4534	CLIP-seq
MIRT1493553	hsa-miR-4641	CLIP-seq
MIRT2148778	hsa-miR-3165	CLIP-seq
MIRT2148779	hsa-miR-3179	CLIP-seq
MIRT2148780	hsa-miR-4695-5p	CLIP-seq
MIRT2148781	hsa-miR-4790-3p	CLIP-seq
MIRT2148782	hsa-miR-765	CLIP-seq
MIRT2463526	hsa-miR-3183	CLIP-seq
MIRT2463527	hsa-miR-4723-3p	CLIP-seq
MIRT2463528	hsa-miR-500a	CLIP-seq

Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001942	Process	Hair follicle development	IMP	17847007, 19559398
GO:0005102	Function	Signaling receptor binding	IEA
GO:0005109	Function	Frizzled binding	IBA
GO:0005125	Function	Cytokine activity	IBA
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA
GO:0010628	Process	Positive regulation of gene expression	IEA
GO:0014033	Process	Neural crest cell differentiation	IEA
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0030182	Process	Neuron differentiation	IBA
GO:0031069	Process	Hair follicle morphogenesis	IMP	20163410
GO:0042476	Process	Odontogenesis	IMP	17847007, 19559398
GO:0042487	Process	Regulation of odontogenesis of dentin-containing tooth	IEA
GO:0043586	Process	Tongue development	IMP	17847007, 19559398
GO:0043588	Process	Skin development	IMP	17847007, 19559398
GO:0045165	Process	Cell fate commitment	IBA
GO:0048018	Function	Receptor ligand activity	IDA	28733458
GO:0048513	Process	Animal organ development	IEA
GO:0048730	Process	Epidermis morphogenesis	IMP	20163410
GO:0048733	Process	Sebaceous gland development	IMP	19559398
GO:0060070	Process	Canonical Wnt signaling pathway	IBA
GO:0060070	Process	Canonical Wnt signaling pathway	IDA	28733458
GO:0071560	Process	Cellular response to transforming growth factor beta stimulus	IEP	15040835

MIM	HGNC	e!Ensembl
606268	13829	ENSG00000135925

Q9GZT5

Protein name

Protein Wnt-10a

Protein function

Ligand for members of the frizzled family of seven transmembrane receptors (Probable). Functions in the canonical Wnt/beta-catenin signaling pathway (By similarity). Plays a role in normal ectoderm development (PubMed:17847007, PubMed:28589954).

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00110	wnt	63 → 417	wnt family	Family

Sequence

MGSAHPRPWLRLRPQPQPRPALWVLLFFLLLLAAAMPRSAPNDILDLRLPPEPVLNANTV
CLTLPGLSRRQMEVCVRHPDVAASAIQGIQIAIHECQHQFRDQRWNCSSLETRNKIPYES
PIFSRGFRESAFAYAIAAAGVVHAVSNACALGKLKACGCDASRRGDEEAFRRKLHRLQLD
ALQRGKGLSHGVPEHPALPTASPGLQDSWEWGGCSPDMGFGERFSKDFLDSREPHRDIHA
RMRLHNNRVGRQAVMENMRRKCKCHGTSGSCQLKTCWQVTPEFRTVGALLRSRFHRATLI
RPHNRNGGQLEPGPAGAPSPAPGAPGPRRRASPADLVYFEKSPDFCEREPRLDSAGTVGR
LCNKSSAGSDGCGSMCCGRGHNILRQTRSERCHCRFHWCCFVVCEECRITEWVSVCK

Sequence length

417

Interactions

View interactions

	KEGG		Reactome
	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 Basal cell carcinoma Breast cancer Hepatocellular carcinoma Gastric cancer		WNT ligand biogenesis and trafficking

1204

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ectodermal dysplasia	Likely pathogenic; Pathogenic	rs121908119	RCV001729335
Ectodermal dysplasia WNT10A related	Likely pathogenic; Pathogenic	rs121908119	RCV006249547
Odonto-onycho-dermal dysplasia	Likely pathogenic; Pathogenic	rs746813123, rs2106010718, rs2106011673, rs886055642, rs561173643, rs2106016170, rs2106016375, rs2106018205, rs2106018239, rs1559416138, rs2106018397, rs1203128182, rs2106018559, rs2106018717, rs1944675271 View all (74 more)	RCV001378317 RCV001390604 RCV001382583 RCV001388708 RCV001388812 RCV001386230 RCV001382570 RCV001387650 RCV001389202 RCV001386374 RCV001389023 RCV001384812 RCV001387962 RCV001910237 RCV001910291 RCV001923484 RCV002037900 RCV001963872 RCV002002481 RCV002005566 RCV001956186 RCV001901602 RCV001929713 RCV003051281 RCV003075306 RCV000004714 RCV000004715 RCV000004718 RCV000004719 RCV000004720 RCV002580474 RCV002590808 RCV002681329 RCV002889159 RCV002898625 RCV002894342 RCV002877108 RCV002937282 RCV002979218 RCV002994875 RCV003048075 RCV003056185 RCV000804067 RCV000677100 RCV001855007 RCV003323311 RCV003777343 RCV003327602 RCV005419614 RCV003777344 RCV003780037 RCV003780038 RCV003792702 RCV003806984 RCV003791517 RCV003804038 RCV003804194 RCV003804248 RCV003799669 RCV003801220 RCV003809292 RCV003810061 RCV003812882 RCV003802505 RCV004577640 RCV001232141 RCV000477883 RCV005355978 RCV001379319 RCV000525525 RCV000551493 RCV000639735 RCV000639737 RCV000677101 RCV000677103 RCV000677099 RCV000677102 RCV000686716 RCV000792132 RCV000818549 RCV000811807 RCV000995914 RCV001044079 RCV001044035 RCV001047325 RCV001069353 RCV001194666 RCV001211943 RCV001204324 RCV001205643 RCV001228664 RCV001241317
	Likely pathogenic; Pathogenic	rs2106018205, rs1234227647, rs1221516695, rs1249944381, rs121908119, rs121908121, rs372993798, rs886039453, rs886039454, rs1060499588, rs1085308031, rs543063101, rs762739726, rs764658964, rs1434390821 View all (6 more)	RCV005014540 RCV005606957 RCV005025545 RCV005017009 RCV000004716 RCV005016239 RCV001814131 RCV001275115 RCV002503967 RCV000477883 RCV005355978 RCV001275114 RCV000763071 RCV005019061 RCV001835029 RCV005628840 RCV005606701 RCV002507361 RCV001275113 RCV002497378 RCV001828648
Tooth agenesis, selective, 4	Likely pathogenic; Pathogenic	rs746813123, rs2106010718, rs2106011673, rs886055642, rs561173643, rs2106016170, rs2106016375, rs2106018205, rs2106018239, rs1559416138, rs2106018397, rs1203128182, rs2106018559, rs2106018717, rs1944675271 View all (69 more)	RCV001378317 RCV001390604 RCV001382583 RCV001388708 RCV001388812 RCV001386230 RCV001382570 RCV001387650 RCV001389202 RCV001386374 RCV001389023 RCV001384812 RCV001387962 RCV001910237 RCV001910291 RCV001923484 RCV002037900 RCV001963872 RCV002002481 RCV002005566 RCV001956186 RCV001901602 RCV001929713 RCV002286330 RCV002510236 RCV003051281 RCV003075306 RCV001851651 RCV000030650 RCV000030651 RCV003764526 RCV002580474 RCV002590808 RCV002681329 RCV002889159 RCV002898625 RCV002894342 RCV002877108 RCV002937282 RCV002979218 RCV002994875 RCV003048075 RCV003056185 RCV000804067 RCV000823047 RCV001855007 RCV003323310 RCV003323312 RCV003323313 RCV003324106 RCV003324107 RCV003780037 RCV003780038 RCV003792702 RCV003806984 RCV003791517 RCV003804038 RCV003804194 RCV003804248 RCV003799669 RCV003801220 RCV003809292 RCV003810061 RCV003812882 RCV003802505 RCV001232141 RCV000477883 RCV005355978 RCV001379319 RCV000525525 RCV000551493 RCV000639735 RCV000639737 RCV001868287 RCV000686716 RCV000792132 RCV000818549 RCV000811807 RCV001044079 RCV001044035 RCV001047325 RCV001069353 RCV001211943 RCV001204324 RCV001205643 RCV001228664 RCV001241317
WNT10A-related disorder	Likely pathogenic; Pathogenic	rs121908119, rs886039453, rs2470312725, rs318240759	RCV000779308 RCV004535236 RCV004539484 RCV004542736

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Abnormality of the dentition	Uncertain significance	rs563548971, rs978088338	RCV002254493 RCV002254494
Arthralgia	Uncertain significance	rs149245953	RCV000415098
Bladder exstrophy-epispadias-cloacal extrophy complex	Conflicting classifications of pathogenicity	rs368280129	RCV000172902
Glioma susceptibility 1	Likely benign	rs148979463	RCV005896110
Hypohidrotic ectodermal dysplasia	Conflicting classifications of pathogenicity	rs121908120	RCV000754840
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	rs201578578	RCV005913859
Palmoplantar keratoderma	Uncertain significance	rs149245953	RCV000415098
See cases	Conflicting classifications of pathogenicity	rs121908120	RCV004584315
Selective tooth agenesis	Uncertain significance; Likely benign	rs762914440, rs886055636, rs571829301, rs561005501, rs886055633, rs556182426, rs138370318, rs886055641, rs886055634, rs886055635, rs774035749, rs886055638, rs886055639, rs886055640, rs148979463	RCV000327931 RCV000287393 RCV000313367 RCV000393221 RCV000285189 RCV000342611 RCV000385171 RCV000282018 RCV000336880 RCV000276465 RCV000378266 RCV000390295 RCV000361608 RCV000317473 RCV000389567
Squamous cell carcinoma of the head and neck	Conflicting classifications of pathogenicity	rs201578578	RCV005913858
Stiff skin	Uncertain significance	rs149245953	RCV000415098
Tooth agenesis	Conflicting classifications of pathogenicity	rs147680216, rs121908120, rs77583146, rs34972707	RCV000845115 RCV000845113 RCV000845116 RCV000845114
Tooth agenesis, selective, 2	Conflicting classifications of pathogenicity	rs147680216, rs116998555	RCV003233110 RCV003233498

Show/Hide Text Mining Associations (64)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenoma	Associate	21547848
Alopecia	Associate	23358095, 34118813, 34506541
Alopecia Areata	Associate	34118813
Amelogenesis imperfecta local hypoplastic form	Associate	35537890
Anodontia	Associate	19471313, 22581971, 23227268, 23991204, 24312213, 24631698, 24700731, 26964878, 27049303, 27665865, 27881089, 28813618, 28944914, 30046887, 31652981 View all (5 more)
Anodontia of Permanent Dentition	Associate	26964878
Autoimmune Diseases	Associate	34118813
Breast Neoplasms	Associate	23372744
Calcinosis	Associate	36605938
Carcinogenesis	Associate	17767013, 24631698
Carcinogenesis	Stimulate	23094073
Carcinoma Renal Cell	Stimulate	23094073
Cholangiocarcinoma	Stimulate	39831920
Conversion Disorder	Associate	36017684
Cysts	Associate	19559398
Deafness	Associate	28944914
Deafness Autosomal Recessive	Associate	30046887
Deafness oligodontia syndrome	Associate	19559398, 24312213, 26387593, 27650966, 27881089, 31652981, 34228861, 34593752, 37422997
Dental Pulp Calcification	Associate	37566620
Dry Eye Syndromes	Associate	19471313
Eccrine Syringofibroadenomatosis with Eyelid Abnormalities	Associate	26964878
Ectodermal Dysplasia	Associate	17847007, 19559398, 24700731, 26964878, 27049303, 27881089, 28944914, 30974434, 31796081, 34118813, 36421794
Ectodermal Dysplasia 1 Anhidrotic	Associate	24312213, 38280992
Ectodermal Dysplasia Hypohidrotic Autosomal Recessive	Associate	30974434
Fibrosis	Associate	25054240, 29955137
Genetic Diseases Inborn	Associate	22581971
Gomez Lopez Hernandez syndrome	Associate	17847007, 19471313, 19559398, 24398796, 24700731, 26964878
Hairy palms and soles	Associate	19471313, 27881089
Hamman Rich Syndrome	Associate	25054240
Hydatidiform Mole	Associate	37566620
Hyperhidrosis	Associate	26964878
Hypogonadism	Associate	28944914
Hypophosphatasia	Associate	39519277
Intervertebral Disc Degeneration	Associate	33090383
Keratoconus	Associate	26049155, 33988693
Kidney Diseases	Associate	25054240
Leukemia Lymphocytic Chronic B Cell	Associate	14973184
Leukemia Myeloid Acute	Associate	17767013, 37885041
Microphthalmia syndromic 2	Associate	30046887
Muscular Dystrophy Congenital Megaconial Type	Associate	36017684
Nail Diseases	Associate	19471313
Nail Patella Syndrome	Associate	19471313, 24312213
Nails Malformed	Associate	27881089, 36421794
Neoplasms	Associate	25054240, 35704796
Nephritis Interstitial	Associate	25054240
Neural crest tumor	Associate	31796081
Odontoonychodermal dysplasia	Associate	22581971
Papillary Thyroid Microcarcinoma	Associate	36605938
Precursor B Cell Lymphoblastic Leukemia Lymphoma	Associate	22426169
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	22426169, 33417298
Radiculopathy	Associate	35537890
Retinal Dysplasia	Associate	22581971
Schopf Schulz Passarge Syndrome	Associate	19559398, 24312213, 24398796, 26964878
Scoliosis	Associate	34440365
Signs and Symptoms	Associate	27881089
Skin Abnormalities	Associate	28944914
Skin Neoplasms	Associate	19559398
Taurodontism	Associate	37422997
Thyroid Cancer Papillary	Inhibit	37208504
Tooth Abnormalities	Associate	19559398
Tooth Agenesis Selective 4	Associate	24700731, 30046887
Urinary Bladder Neoplasms	Associate	26722457
Witkop syndrome	Associate	19559398
Zlotogora Ogur syndrome	Associate	17847007

WNT10A (Wnt family member 10A)