WNT5B

Summary

WNT5B (Wnt family member 5B, HGNC:16265) is a protein-coding gene on chromosome 12p13.33, encoding Protein Wnt-5b (Q9H1J7). Ligand for members of the frizzled family of seven transmembrane receptors.

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 94% and 80% amino acid identity to the mouse Wnt5b protein and the human WNT5A protein, respectively. Alternative splicing of this gene generates 2 transcript variants.

Source: NCBI Gene 81029 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_032642

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16265
Approved symbol	WNT5B
Name	Wnt family member 5B
Location	12p13.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000111186
Ensembl biotype	protein_coding
OMIM	606361
Entrez	81029

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 21 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000310594, ENST00000397196, ENST00000537031, ENST00000538854, ENST00000539198, ENST00000542408, ENST00000543071, ENST00000543563, ENST00000545747, ENST00000545811, ENST00000861256, ENST00000861257, ENST00000861258, ENST00000861259, ENST00000861260, ENST00000861261, ENST00000861262, ENST00000861263, ENST00000861264, ENST00000861265, ENST00000935027, ENST00000969384, ENST00000969385, ENST00000969386

RefSeq mRNA: 2 — MANE Select: NM_032642 NM_030775, NM_032642

CCDS: CCDS8510

Canonical transcript exons

ENST00000397196 — 5 exons

Exon	Start	End
ENSE00000712187	1639684	1639976
ENSE00000816803	1632658	1632905
ENSE00001527637	1645794	1647212
ENSE00001527638	1629231	1629371
ENSE00003512366	1631298	1631434

Expression profiles

Bgee: expression breadth ubiquitous, 192 present calls, max score 96.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.5580 / max 359.5841, expressed in 1139 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
123363	9.8650	1073
123375	0.2632	84
123372	0.1811	68
123377	0.0843	24
123379	0.0659	29
123371	0.0382	6
123376	0.0238	7
123373	0.0142	4
123378	0.0117	4
123374	0.0106	1

Top tissues by expression

267 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	96.59	gold quality
lower esophagus muscularis layer	UBERON:0035833	90.39	gold quality
lower esophagus	UBERON:0013473	90.38	gold quality
lower esophagus mucosa	UBERON:0035834	87.49	gold quality
esophagus	UBERON:0001043	86.99	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	86.56	gold quality
periodontal ligament	UBERON:0008266	86.11	gold quality
prostate gland	UBERON:0002367	85.80	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.82	gold quality
esophagus mucosa	UBERON:0002469	84.36	gold quality
esophagus squamous epithelium	UBERON:0006920	83.83	gold quality
minor salivary gland	UBERON:0001830	83.66	gold quality
epithelium of esophagus	UBERON:0001976	83.39	gold quality
palpebral conjunctiva	UBERON:0001812	83.31	gold quality
saliva-secreting gland	UBERON:0001044	82.05	gold quality
tibia	UBERON:0000979	81.44	gold quality
mouth mucosa	UBERON:0003729	81.39	gold quality
ventricular zone	UBERON:0003053	80.12	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	79.81	gold quality
eye	UBERON:0000970	79.79	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.40	gold quality
pituitary gland	UBERON:0000007	79.22	gold quality
adenohypophysis	UBERON:0002196	78.73	gold quality
mucosa of transverse colon	UBERON:0004991	78.72	gold quality
cortical plate	UBERON:0005343	78.50	gold quality
calcaneal tendon	UBERON:0003701	78.20	gold quality
buccal mucosa cell	CL:0002336	78.11	silver quality
tibial nerve	UBERON:0001323	78.07	gold quality
urinary bladder	UBERON:0001255	77.80	gold quality
seminal vesicle	UBERON:0000998	77.45	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.88

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CNBP, SMARCA5, TBX2

miRNA regulators (miRDB)

58 targeting WNT5B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-4645-3P	99.76	69.33	993
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-548AV-3P	99.43	68.50	1721
HSA-MIR-6871-3P	99.43	68.85	741
HSA-MIR-4316	99.37	65.75	1360

Literature-anchored findings (GeneRIF, showing 36)

• WNT5b is upregulated by beta-estradiol in tumor cell lines (PMID:12165812)
• WNT5B gene may contribute to conferring susceptibility to type 2 diabetes and may be involved in the pathogenesis of this disease through the regulation of adipocyte function. (PMID:15386214)
• In leiomyoma cells, the regulation of Wnt5b expression by retinoids appears to be attenuated. (PMID:15972578)
• Variation in WNT5B predisposes to type 2 diabetes in the absence of obesity. (PMID:18555673)
• Results demonstrated significant up-regulation of WNT-3, WNT-4, WNT-5B, WNT-7B, WNT-9A, WNT-10A, and WNT-16B in patients with CLL compared to normal subjects. (PMID:19863181)
• This is significantly related to fat cell differentiation, suggesting its possible involvement in the onset of diabetes mellitus type 2 and metabolic syndrome. (PMID:21766608)
• Differentiation paralleled the activation of Wnt5/Calmodulin signalling by autocrine/paracrine intense secretion of Wnt5a and Wnt5b (PMID:21980498)
• This study shows that the WNT5B germline variant rs2010851 was significantly identified as a stage-dependent prognostic marker for CC patients after 5-fluorouracil-based adjuvant therapy. (PMID:23817222)
• TGF-beta/Smad, integrin/integrin-linked kinase (ILK) and wnt/beta-catenin signaling pathways are involved in epithelial to mesenchymal transition in human renal fibrogenesis. (PMID:24040439)
• These results indicate that Wnt5b is involved in the migration ability of OSCC cells through active Cdc42 and RhoA. (PMID:24220306)
• WNT3 and WNT5B are critical factors, secreted from mesenchymal cancer cells, for instigating the epithelial cancer cell invasion. (PMID:24344732)
• Ursolic acid suppressed the expression of Wnt5alpha/beta and beta-catenin, inducing apoptosis in prostate cancer cells. (PMID:24399733)
• WNT5B is elevated in both in the tumor and the patients’ serum from triple negative breast cancer. (PMID:24564888)
• Knocking down Wnt5b expression reduced phospho-PKCA levels and cell migration. (PMID:24841200)
• Report increased Wnt5b levels in adriamycin treated liver cancer stem cells within 4h of treatment. (PMID:24944491)
• Results demonstrate that the Wnt5B pathway may play an important role in atypical teratoid rhabdoid tumor biology. (PMID:25246426)
• The interaction between Wnt isoforms and their LRP6 cognate receptor depends on the jutting loop present in Wnt3a but absent in Wnt5b. (PMID:25425204)
• This study identified WNT5B and CTNNBL1 for peak bone mineral density and body composition in males from the Han Chinese ethnic group. (PMID:26733379)
• these results suggest that TGF-beta1 stimulates HSC-4 cell invasion through the Slug/Wnt-5b/MMP-10 signalling axis. (PMID:26861993)
• WNT-5B induces IL-6 and CXCL8 secretion in pulmonary fibroblasts. (PMID:27036869)
• overexpression of WNT5B significantly increased cell proliferation, migration and invasion capacities of the COLO 205 cells in vitro. WNT5B may play an important role in the tumorigenesis of colorectal cancer. (PMID:27121420)
• exaggerated WNT-5B expression upon cigarette smoke exposure in the bronchial epithelium of COPD patients leads to TGF-beta/Smad3-dependent expression of genes related to airway remodelling (PMID:27126693)
• the data suggest that WNT5B induces tube formation by regulating the expression of Snail and Slug proteins through activation of canonical and non-canonical WNT signalling pathways. (PMID:27593938)
• results suggest that Wnt5b-associated exosomes promote cancer cell migration and proliferation in a paracrine manner (PMID:27762090)
• Noncanonical Wnt signaling via Wnt5a/5b/11 may have role in the pathogenesis of aortic valve calcification. (PMID:27932350)
• were not able to replicate or further verify the genetic association of polymorphisms in WNT4 and WNT5B with bone mineral density (PMID:28078366)
• IMP3 also facilitates the transcription of SLUG, which is necessary for TAZ nuclear localization and activation, by a mechanism that is also mediated by WNT5B. (PMID:29847788)
• WNT5B exerts oncogenic effects and is negatively regulated by miR-5587-3p in lung adenocarcinoma progression. (PMID:31666682)
• Up-regulated miR-374a-3p relieves lipopolysaccharides induced injury in CHON-001 cells via regulating Wingless-type MMTV integration site family member 5B. (PMID:32092330)
• The lncRNA RP11-142A22.4 promotes adipogenesis by sponging miR-587 to modulate Wnt5beta expression. (PMID:32561739)
• Exosome-mediated circ_0001846 participates in IL-1beta-induced chondrocyte cell damage by miR-149-5p-dependent regulation of WNT5B. (PMID:34536574)
• Estrogen receptor alpha and NFATc1 bind to a bone mineral density-associated SNP to repress WNT5B in osteoblasts. (PMID:34906330)
• DLL4/Notch3/WNT5B axis mediates bidirectional prometastatic crosstalk between melanoma and lymphatic endothelial cells. (PMID:37971882)
• Role of Wnt5b-Ror1 signaling in the proliferation of pancreatic ductal adenocarcinoma cells. (PMID:38531660)
• WNT5B drives osteosarcoma stemness, chemoresistance and metastasis. (PMID:38689429)
• WNT5B promotes the malignant phenotype of non-small cell lung cancer via the FZD3-DVL3-RAC1-PCP-JNK pathway. (PMID:39094673)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	wnt5b	ENSDARG00000102464
mus_musculus	Wnt5b	ENSMUSG00000030170
rattus_norvegicus	Wnt5b	ENSRNOG00000008168
drosophila_melanogaster	Wnt2	FBGN0004360
drosophila_melanogaster	Wnt5	FBGN0010194
drosophila_melanogaster	Wnt10	FBGN0031903
caenorhabditis_elegans		WBGENE00000857
caenorhabditis_elegans		WBGENE00000858
caenorhabditis_elegans	lin-44	WBGENE00003029

Paralogs (18): WNT16 (ENSG00000002745), WNT8A (ENSG00000061492), WNT8B (ENSG00000075290), WNT11 (ENSG00000085741), WNT2 (ENSG00000105989), WNT3 (ENSG00000108379), WNT5A (ENSG00000114251), WNT6 (ENSG00000115596), WNT1 (ENSG00000125084), WNT2B (ENSG00000134245), WNT10A (ENSG00000135925), WNT9A (ENSG00000143816), WNT3A (ENSG00000154342), WNT7A (ENSG00000154764), WNT9B (ENSG00000158955), WNT4 (ENSG00000162552), WNT10B (ENSG00000169884), WNT7B (ENSG00000188064)

Protein

Protein identifiers

Protein Wnt-5b — Q9H1J7 (reviewed: Q9H1J7)

All UniProt accessions (5): Q9H1J7, F5GYM2, F5H034, F5H364, F5H7Q6

UniProt curated annotations — full annotation on UniProt →

Function. Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters.

Subunit / interactions. Interacts with PORCN.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Post-translational modifications. Palmitoleoylation is required for efficient binding to frizzled receptors. Depalmitoleoylation leads to Wnt signaling pathway inhibition.

Similarity. Belongs to the Wnt family.

RefSeq proteins (2): NP_110402, NP_116031* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005817	Wnt	Family
IPR018161	Wnt_CS	Conserved_site
IPR043158	Wnt_C	Homologous_superfamily

Pfam: PF00110

UniProt features (24 total): disulfide bond 11, sequence conflict 6, glycosylation site 4, signal peptide 1, chain 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H1J7-F1	89.83	0.80

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 223

Disulfide bonds (11): 217–231, 219–226, 288–319, 304–314, 318–358, 334–349, 336–346, 341–342, 83–94, 133–141, 143–161

Glycosylation sites (4): 93, 99, 291, 305

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-3238698	WNT ligand biogenesis and trafficking
R-HSA-4086400	PCP/CE pathway

MSigDB gene sets: 263 (showing top): GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_LENS_FIBER_CELL_DIFFERENTIATION, GOBP_EPITHELIUM_DEVELOPMENT, LEE_NEURAL_CREST_STEM_CELL_DN, GOBP_REGULATION_OF_FAT_CELL_DIFFERENTIATION, BENPORATH_ES_WITH_H3K27ME3, GOBP_CARTILAGE_DEVELOPMENT, KEGG_HEDGEHOG_SIGNALING_PATHWAY, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_EPITHELIAL_CELL_DEVELOPMENT, PEREZ_TP63_TARGETS, GOBP_NON_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_FAT_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_NON_CANONICAL_WNT_SIGNALING_PATHWAY

GO Biological Process (15): chondrocyte differentiation (GO:0002062), neuron differentiation (GO:0030182), positive regulation of cell migration (GO:0030335), muscle cell differentiation (GO:0042692), cell fate commitment (GO:0045165), fat cell differentiation (GO:0045444), positive regulation of fat cell differentiation (GO:0045600), canonical Wnt signaling pathway (GO:0060070), lens fiber cell development (GO:0070307), cellular response to retinoic acid (GO:0071300), negative regulation of canonical Wnt signaling pathway (GO:0090090), positive regulation of convergent extension involved in gastrulation (GO:1904105), positive regulation of non-canonical Wnt signaling pathway (GO:2000052), multicellular organism development (GO:0007275), Wnt signaling pathway (GO:0016055)

GO Molecular Function (3): signaling receptor binding (GO:0005102), frizzled binding (GO:0005109), cytokine activity (GO:0005125)

GO Cellular Component (9): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), endoplasmic reticulum lumen (GO:0005788), Golgi lumen (GO:0005796), plasma membrane (GO:0005886), cell surface (GO:0009986), endocytic vesicle membrane (GO:0030666), extracellular matrix (GO:0031012), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Signaling by WNT	1
Beta-catenin independent WNT signaling	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell differentiation	5
cellular anatomical structure	2
intracellular organelle lumen	2
cartilage development	1
generation of neurons	1
cell migration	1
regulation of cell migration	1
positive regulation of cell motility	1
muscle structure development	1
cellular developmental process	1
fat cell differentiation	1
positive regulation of cell differentiation	1
regulation of fat cell differentiation	1
Wnt signaling pathway	1
epithelial cell development	1
lens fiber cell differentiation	1
response to retinoic acid	1
cellular response to lipid	1
cellular response to oxygen-containing compound	1
negative regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
regulation of canonical Wnt signaling pathway	1
convergent extension involved in gastrulation	1
regulation of convergent extension involved in gastrulation	1
positive regulation of morphogenesis of an epithelium	1
positive regulation of Wnt signaling pathway	1
non-canonical Wnt signaling pathway	1
regulation of non-canonical Wnt signaling pathway	1
multicellular organismal process	1
anatomical structure development	1
cell surface receptor signaling pathway	1
protein binding	1
G protein-coupled receptor binding	1
receptor ligand activity	1
endoplasmic reticulum	1
Golgi apparatus	1
membrane	1
cell periphery	1
endocytic vesicle	1
cytoplasmic vesicle membrane	1

Protein interactions and networks

STRING

1446 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WNT5B	FZD4	Q9ULV1	900
WNT5B	FZD6	O60353	894
WNT5B	FZD8	Q9H461	863
WNT5B	FZD2	Q14332	852
WNT5B	FZD9	O00144	846
WNT5B	FZD3	Q9NPG1	834
WNT5B	MMP3	P08254	819
WNT5B	FOXN1	O15353	813
WNT5B	FZD7	O75084	804
WNT5B	FZD5	Q13467	800
WNT5B	RYK	P34925	790
WNT5B	LRP6	O75581	713
WNT5B	MAFB	Q9Y5Q3	707
WNT5B	SFRP1	Q8N474	702
WNT5B	SFRP4	Q6FHJ7	662

IntAct

7 interactions, top by confidence:

A	B	Type	Score
KLRG2	GXYLT2	psi-mi:“MI:0914”(association)	0.530
WNT5B	WLS	psi-mi:“MI:0915”(physical association)	0.400
APPBP2	WNT5B	psi-mi:“MI:0915”(physical association)	0.370
WNT5A	POTEF	psi-mi:“MI:0914”(association)	0.350

BioGRID (7): WNT5B (Two-hybrid), WNT5B (Affinity Capture-MS), WNT5B (Affinity Capture-MS), WNT5B (Affinity Capture-MS), WNT5B (Affinity Capture-MS), WNT5B (Cross-Linking-MS (XL-MS)), WNT5B (Protein-RNA)

ESM2 similar proteins: A0M8S1, A0M8T2, A1X153, A4D7S0, O00755, P09544, P21552, P22725, P22726, P28465, P87387, Q07DV4, Q07DW8, Q07DX7, Q07DY7, Q07DZ8, Q07E18, Q07E31, Q07E44, Q09YI4, Q09YJ6, Q09YK7, Q09YN1, Q108U2, Q1KYK4, Q1KYK5, Q1KYK6, Q1KYK7, Q1KYK9, Q1KYL1, Q2IBB0, Q2IBB5, Q2IBE2, Q2IBF4, Q2IBG1, Q2QL76, Q2QL85, Q2QL96, Q2QLA5, Q2QLB6

Diamond homologs: A0M8S1, A0M8T2, A1X153, A4D7S0, B2GUT4, O00755, O13267, O15978, O42122, O70283, P04426, P04628, P09544, P09615, P10108, P17553, P21551, P21552, P22724, P22725, P22726, P22727, P24257, P24383, P27467, P28047, P28465, P31285, P31286, P33945, P34888, P34889, P41221, P43446, P47793, P49337, P49338, P49339, P49340, P49893

SIGNOR signaling

7 interactions.

A	Effect	B	Mechanism
WNT5B	up-regulates	FZD3	binding
WNT5B	up-regulates	LRP5	binding
WNT5B	up-regulates	LRP6	binding
WNT5B	up-regulates	FZD6	binding
WNT5B	up-regulates	PPARG
SOSTDC1	“down-regulates activity”	WNT5B

Disease & clinical

Clinical variants and AI predictions

ClinVar

47 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2611 predictions. Top by Δscore:

Variant	Effect	Δscore
12:1574842:G:GG	donor_gain	1.0000
12:1632643:G:A	acceptor_gain	1.0000
12:1632901:GATAG:G	donor_gain	1.0000
12:1632903:TAGG:T	donor_loss	1.0000
12:1632904:AGGT:A	donor_loss	1.0000
12:1632905:GGTAA:G	donor_loss	1.0000
12:1632906:GTAAG:G	donor_loss	1.0000
12:1632907:T:A	donor_loss	1.0000
12:1639975:GG:G	donor_gain	1.0000
12:1639976:GG:G	donor_gain	1.0000
12:1645790:CTAG:C	acceptor_loss	1.0000
12:1645791:TAG:T	acceptor_loss	1.0000
12:1645792:A:AG	acceptor_gain	1.0000
12:1645792:AG:A	acceptor_gain	1.0000
12:1645792:AGGCT:A	acceptor_gain	1.0000
12:1645793:G:GG	acceptor_gain	1.0000
12:1645793:GG:G	acceptor_gain	1.0000
12:1645793:GGC:G	acceptor_gain	1.0000
12:1645793:GGCT:G	acceptor_gain	1.0000
12:1645793:GGCTG:G	acceptor_gain	1.0000
12:1574837:GTCAT:G	donor_gain	0.9900
12:1574840:ATG:A	donor_loss	0.9900
12:1574841:TGT:T	donor_loss	0.9900
12:1574842:G:GC	donor_loss	0.9900
12:1574843:TG:T	donor_loss	0.9900
12:1574844:GA:G	donor_loss	0.9900
12:1574845:AGT:A	donor_loss	0.9900
12:1631292:CTCCA:C	acceptor_loss	0.9900
12:1631293:TCCA:T	acceptor_loss	0.9900
12:1631295:CA:C	acceptor_loss	0.9900

AlphaMissense

2356 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:1632851:T:A	W92R	1.000
12:1632851:T:C	W92R	1.000
12:1632853:G:C	W92C	1.000
12:1632853:G:T	W92C	1.000
12:1639753:G:A	C133Y	1.000
12:1639827:T:A	W158R	1.000
12:1639827:T:C	W158R	1.000
12:1639829:G:C	W158C	1.000
12:1639829:G:T	W158C	1.000
12:1639879:T:G	F175C	1.000
12:1645826:A:C	K218N	1.000
12:1645826:A:T	K218N	1.000
12:1645827:T:A	C219S	1.000
12:1645828:G:C	C219S	1.000
12:1645830:C:G	H220D	1.000
12:1645833:G:T	G221C	1.000
12:1645849:G:A	C226Y	1.000
12:1645864:G:A	C231Y	1.000
12:1645865:C:G	C231W	1.000
12:1646082:T:A	C304S	1.000
12:1646083:G:C	C304S	1.000
12:1646184:T:C	F338L	1.000
12:1646185:T:G	F338C	1.000
12:1646186:C:A	F338L	1.000
12:1646186:C:G	F338L	1.000
12:1646192:G:C	W340C	1.000
12:1646192:G:T	W340C	1.000
12:1632761:T:A	C62S	0.999
12:1632762:G:A	C62Y	0.999
12:1632762:G:C	C62S	0.999

dbSNP variants (sampled 300 via entrez): RS1000028294 (12:1618684 A>G), RS1000212873 (12:1638512 G>T), RS1000247121 (12:1638935 T>C), RS1000371117 (12:1621624 A>C,G), RS1000669682 (12:1628587 C>T), RS1000685816 (12:1630899 G>A,C), RS1000839846 (12:1615292 C>T), RS1000862044 (12:1643528 G>A,T), RS1001081996 (12:1617604 C>G), RS1001118448 (12:1642780 G>A), RS1001406271 (12:1620615 T>G), RS1001445192 (12:1642536 G>A,C), RS1001547181 (12:1643458 C>T), RS1001589020 (12:1631799 T>C), RS1001600006 (12:1638000 G>A,T)

Disease associations

OMIM: gene MIM:606361 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001356_10	Gout	1.000000e-07
GCST001356_11	Gout	1.000000e-07
GCST004781_29	Sulfasalazine-induced agranulocytosis	7.000000e-07
GCST010796_5310	Electrocardiogram morphology (amplitude at temporal datapoints)	7.000000e-09
GCST010796_5311	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-08
GCST010796_5312	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

2 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs12819505	Efficacy	3	Platinum compounds	Non-Small Cell Lung Carcinoma
rs2010851	Other	3	fluorouracil	Colonic Neoplasms

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs2010851	WNT5B	3	2.00	1	fluorouracil
rs12819505	WNT5B	3	3.00	1	Platinum compounds

CTD chemical–gene interactions

54 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	6
bisphenol A	affects cotreatment, increases methylation, decreases expression	3
trichostatin A	affects cotreatment, decreases expression	3
Benzo(a)pyrene	affects response to substance, increases expression, affects methylation, decreases expression, increases methylation	3
mercuric bromide	decreases expression, affects cotreatment	2
entinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Dexamethasone	affects cotreatment, decreases expression	2
Estradiol	decreases expression, increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Progesterone	increases expression, affects cotreatment, decreases expression	2
Smoke	increases expression, decreases expression, increases abundance	2
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	2
Asbestos, Serpentine	decreases methylation, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
bisphenol F	affects cotreatment, decreases expression	1
bufotalin	decreases reaction, increases expression	1
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
sodium arsenite	decreases expression	1
rutecarpine	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
belinostat	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	decreases expression, affects cotreatment	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A7W0	SEES3-1V human WNT5B, clone1	Embryonic stem cell	Male
CVCL_A7W1	SEES3-1V human WNT5B, clone2	Embryonic stem cell	Male
CVCL_A7W2	SEES3-1V human WNT5B, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.