WNT16

Wnt family member 16, the group of Wnt family

Basic information

Region (hg38): 7:121325367-121341104

Links

ENSG00000002745 ∙ NCBI:51384 ∙ OMIM:606267 ∙ HGNC:16267 ∙ Uniprot:Q9UBV4 ∙ 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 WNT16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT16 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			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	2

Variants in WNT16

This is a list of pathogenic ClinVar variants found in the WNT16 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-121329297-A-G		not specified	Uncertain significance (Apr 26, 2024)
7-121329302-G-C		not specified	Uncertain significance (May 01, 2024)
7-121329323-C-G		not specified	Uncertain significance (Jul 31, 2024)
7-121329584-C-T		not specified	Uncertain significance (Sep 30, 2024)
7-121329617-A-G		not specified	Uncertain significance (Feb 28, 2023)
7-121329661-C-T		not specified	Uncertain significance (Jan 26, 2022)
7-121329692-C-A		not specified	Uncertain significance (Dec 27, 2023)
7-121329722-A-G		not specified	Uncertain significance (May 20, 2024)
7-121329732-C-G		not specified	Uncertain significance (Jun 29, 2022)
7-121329737-G-A		not specified	Uncertain significance (May 06, 2022)
7-121329754-A-G		not specified	Likely benign (Aug 21, 2023)
7-121329754-A-T		not specified	Uncertain significance (Sep 09, 2024)
7-121329771-C-A			Benign (Jun 08, 2018)
7-121331783-C-T		not specified	Uncertain significance (Jan 31, 2024)
7-121331899-A-T		not specified	Uncertain significance (Jun 05, 2023)
7-121331929-G-A		not specified	Uncertain significance (Apr 25, 2023)
7-121338929-G-A		not specified	Uncertain significance (Sep 06, 2022)
7-121338935-T-A		not specified	Uncertain significance (Dec 15, 2023)
7-121338960-C-A		not specified	Uncertain significance (Dec 10, 2024)
7-121338983-G-A		not specified	Uncertain significance (Apr 07, 2023)
7-121338990-T-G		not specified	Uncertain significance (May 06, 2024)
7-121339004-T-C		not specified	Uncertain significance (Feb 14, 2023)
7-121339025-T-C			Benign (Apr 26, 2018)
7-121339041-G-A		not specified	Uncertain significance (Oct 19, 2024)
7-121339049-C-T		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT16	protein_coding	protein_coding	ENST00000222462	4	15738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000165	0.667	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.173	215	208	1.03	0.0000106	2395
Missense in Polyphen		69	82.155	0.83988		944
Synonymous	-0.212	85	82.6	1.03	0.00000443	693
Loss of Function	1.07	11	15.5	0.708	7.51e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000622	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
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);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);Transcriptional misregulation in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);WNT-Core;Association Between Physico-Chemical Features and Toxicity Associated Pathways;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 GPCR;Signaling by WNT;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;WNT ligand biogenesis and trafficking;GPCR signaling-G alpha i;Wnt Canonical;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• loftool: 0.833
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.8

Haploinsufficiency Scores

• pHI: 0.0845
• hipred: N
• hipred_score: 0.455
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wnt16
• Phenotype: skeleton phenotype

Zebrafish Information Network

• Gene name: wnt16
• Affected structure: hematopoietic stem cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: optic cup formation involved in camera-type eye development;positive regulation of gene expression;positive regulation of phosphatidylinositol 3-kinase signaling;Wnt signaling pathway;neuron differentiation;keratinocyte differentiation;keratinocyte proliferation;cell fate commitment;positive regulation of JNK cascade;bone remodeling;cardiac epithelial to mesenchymal transition;negative regulation of cell death;replicative senescence;oxidative stress-induced premature senescence
• Cellular component: extracellular region;extracellular space;cytoplasm
• Molecular function: frizzled binding