WNT5B

Wnt family member 5B, the group of Wnt family

Basic information

Region (hg38): 12:1529891-1647212

Links

ENSG00000111186 ∙ NCBI:81029 ∙ OMIM:606361 ∙ HGNC:16265 ∙ Uniprot:Q9H1J7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WNT5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT5B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in WNT5B

This is a list of pathogenic ClinVar variants found in the WNT5B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-1592914-C-T		not specified	Uncertain significance (Jun 10, 2022)
12-1592922-C-T		not specified	Uncertain significance (Feb 11, 2022)
12-1593045-A-G		not specified	Uncertain significance (Dec 14, 2022)
12-1593069-C-T		not specified	Uncertain significance (Aug 30, 2021)
12-1593165-G-C		not specified	Uncertain significance (Dec 27, 2023)
12-1593235-T-C		not specified	Uncertain significance (Mar 14, 2023)
12-1593304-G-A			Benign (Apr 09, 2018)
12-1593384-G-C		not specified	Uncertain significance (May 30, 2024)
12-1593404-C-A		not specified	Uncertain significance (Jun 22, 2023)
12-1593463-G-C		not specified	Uncertain significance (May 29, 2024)
12-1593620-C-G		not specified	Uncertain significance (May 27, 2022)
12-1593686-G-A			Likely benign (Jan 01, 2023)
12-1593796-T-C		not specified	Uncertain significance (Mar 30, 2024)
12-1593907-G-C		not specified	Uncertain significance (Aug 10, 2021)
12-1593927-C-T		not specified	Uncertain significance (Dec 01, 2022)
12-1593988-G-A		not specified	Uncertain significance (Aug 21, 2023)
12-1593988-G-T		not specified	Uncertain significance (Oct 02, 2023)
12-1593993-T-C		not specified	Uncertain significance (May 30, 2024)
12-1594015-C-G		not specified	Uncertain significance (Nov 20, 2023)
12-1631382-G-A		not specified	Uncertain significance (Jan 17, 2024)
12-1631382-G-T		not specified	Uncertain significance (Dec 06, 2022)
12-1632704-G-A		not specified	Uncertain significance (Jun 27, 2022)
12-1632720-G-A		not specified	Uncertain significance (May 18, 2022)
12-1632834-A-G		not specified	Uncertain significance (Jul 19, 2023)
12-1632839-C-T		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT5B	protein_coding	protein_coding	ENST00000397196	4	117353

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.585	0.414	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	176	257	0.686	0.0000184	2331
Missense in Polyphen		71	130.3	0.54488		1108
Synonymous	0.693	104	113	0.917	0.00000892	700
Loss of Function	2.97	3	15.7	0.191	8.20e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000449
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000558	0.0000527
Middle Eastern	0.000167	0.000163
South Asian	0.0000336	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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 (By similarity). {ECO:0000250}.
• Pathway: Gastric cancer - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Breast cancer - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Axon guidance - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Basal cell carcinoma - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Adipogenesis;ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Wnt Signaling in Kidney Disease;EMT transition in Colorectal Cancer;Wnt Signaling Pathway;DNA Damage Response (only ATM dependent);Signaling by WNT;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;PCP/CE pathway;Beta-catenin independent WNT signaling;WNT ligand biogenesis and trafficking;GPCR signaling-G alpha i;Wnt Canonical;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.237

Intolerance Scores

• loftool: 0.410
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.4

Haploinsufficiency Scores

• pHI: 0.119
• hipred: Y
• hipred_score: 0.774
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.865

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Wnt5b
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype

Zebrafish Information Network

• Gene name: wnt5b
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: chondrocyte differentiation;Wnt signaling pathway;neuron differentiation;positive regulation of cell migration;wound healing;cell fate commitment;fat cell differentiation;positive regulation of fat cell differentiation;lens fiber cell development;cellular response to retinoic acid;negative regulation of canonical Wnt signaling pathway
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi lumen;plasma membrane;cell surface;endocytic vesicle membrane;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: signaling receptor binding;frizzled binding