WNT6
Wnt family member 6, the group of Wnt family
Basic information
Region (hg38): 2:218859805-218874233
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT6 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 | 2 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 2 | 0 |
Variants in WNT6
This is a list of pathogenic ClinVar variants found in the WNT6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-218860062-C-G | not specified | Uncertain significance (Aug 16, 2022) | ||
| 2-218871095-G-A | not specified | Uncertain significance (Nov 09, 2023) | ||
| 2-218871127-G-A | not specified | Uncertain significance (Apr 10, 2023) | ||
| 2-218871155-G-A | not specified | Uncertain significance (Dec 15, 2023) | ||
| 2-218871595-C-T | not specified | Uncertain significance (May 26, 2023) | ||
| 2-218871610-C-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 2-218871631-G-A | not specified | Uncertain significance (Aug 06, 2021) | ||
| 2-218871705-C-T | not specified | Likely benign (Jan 23, 2024) | ||
| 2-218871753-G-A | Bladder exstrophy-epispadias-cloacal extrophy complex | Likely benign (Mar 31, 2015) | ||
| 2-218871774-C-A | not specified | Uncertain significance (Oct 06, 2021) | ||
| 2-218871810-G-A | Likely benign (Sep 01, 2022) | |||
| 2-218873385-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 2-218873501-G-C | not specified | Uncertain significance (Jan 26, 2022) | ||
| 2-218873564-G-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 2-218873612-G-C | not specified | Uncertain significance (Jan 11, 2023) | ||
| 2-218873746-C-G | not specified | Uncertain significance (Oct 05, 2023) | ||
| 2-218873747-G-A | not specified | Uncertain significance (Sep 01, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WNT6 | protein_coding | protein_coding | ENST00000233948 | 4 | 14412 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0164 | 0.962 | 125445 | 0 | 4 | 125449 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.73 | 136 | 206 | 0.661 | 0.0000108 | 2235 |
| Missense in Polyphen | 44 | 79.591 | 0.55283 | 862 | ||
| Synonymous | 0.944 | 82 | 93.6 | 0.876 | 0.00000492 | 802 |
| Loss of Function | 2.00 | 5 | 12.7 | 0.393 | 6.10e-7 | 131 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000190 | 0.0000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000655 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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. Together with CAV1 may promote chemoresistance of gastric cancer cells to DNA-damaging anthracycline drugs through the activation of the canonical Wnt receptor signaling pathway. {ECO:0000269|PubMed:22370641}.;
- 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);Wnt signaling pathway - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);LncRNA-mediated mechanisms of therapeutic resistance;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
- 0.227
Haploinsufficiency Scores
- pHI
- 0.323
- hipred
- Y
- hipred_score
- 0.777
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.662
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wnt6
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; embryo 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); reproductive system phenotype;
Gene ontology
- Biological process
- branching involved in ureteric bud morphogenesis;axis specification;positive regulation of gene expression;Wnt signaling pathway;neuron differentiation;odontogenesis of dentin-containing tooth;cell fate commitment;positive regulation of transcription, DNA-templated;epithelial-mesenchymal cell signaling;cornea development in camera-type eye;positive regulation of tooth mineralization;cellular response to retinoic acid;nephron tubule formation
- Cellular component
- extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi lumen;plasma membrane;cell surface;endocytic vesicle membrane;extracellular matrix;extracellular exosome
- Molecular function
- frizzled binding