WNT11
Wnt family member 11, the group of Wnt family
Basic information
Region (hg38): 11:76186325-76210736
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 WNT11 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 | 5 | |||||
| missense | 16 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 2 | 5 |
Variants in WNT11
This is a list of pathogenic ClinVar variants found in the WNT11 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-76187081-C-T | not specified | Uncertain significance (Jan 23, 2023) | ||
| 11-76187147-C-T | not specified | Uncertain significance (Mar 29, 2024) | ||
| 11-76187159-C-T | not specified | Uncertain significance (Mar 15, 2024) | ||
| 11-76187168-T-C | not specified | Uncertain significance (Jan 08, 2024) | ||
| 11-76187183-C-T | Bladder exstrophy-epispadias-cloacal extrophy complex | Uncertain significance (Mar 31, 2015) | ||
| 11-76187205-A-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 11-76187208-T-C | Hypospadias | Uncertain significance (Feb 06, 2022) | ||
| 11-76187211-C-T | not specified | Uncertain significance (Aug 21, 2023) | ||
| 11-76191641-C-A | Benign (Aug 20, 2018) | |||
| 11-76191641-C-T | Benign (Dec 31, 2019) | |||
| 11-76191655-G-T | not specified | Uncertain significance (Jan 23, 2023) | ||
| 11-76191700-T-G | not specified | Uncertain significance (Feb 07, 2023) | ||
| 11-76191705-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
| 11-76191735-C-T | not specified | Uncertain significance (Sep 28, 2022) | ||
| 11-76191793-G-T | not specified | Uncertain significance (May 17, 2023) | ||
| 11-76191821-G-A | Benign (May 24, 2018) | |||
| 11-76194596-G-A | not specified | Uncertain significance (May 23, 2023) | ||
| 11-76194713-C-T | not specified | Uncertain significance (Apr 13, 2023) | ||
| 11-76194737-C-G | not specified | Uncertain significance (Apr 18, 2023) | ||
| 11-76194803-C-T | Benign (Dec 31, 2019) | |||
| 11-76194825-G-A | WNT11-related disorder | Likely benign (May 17, 2022) | ||
| 11-76196586-G-A | Benign (May 18, 2018) | |||
| 11-76196604-C-T | WNT11-related disorder • Bladder exstrophy-epispadias-cloacal extrophy complex | Benign (-) | ||
| 11-76196620-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 11-76206330-C-G | not specified | Uncertain significance (Dec 19, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WNT11 | protein_coding | protein_coding | ENST00000322563 | 5 | 24412 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00644 | 0.976 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.41 | 169 | 229 | 0.738 | 0.0000154 | 2238 |
| Missense in Polyphen | 77 | 113.09 | 0.68087 | 1074 | ||
| Synonymous | 0.703 | 92 | 101 | 0.911 | 0.00000725 | 718 |
| Loss of Function | 2.08 | 6 | 14.6 | 0.412 | 8.04e-7 | 161 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000625 | 0.0000462 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000654 | 0.0000653 |
| 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.;
- 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);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;PCP/CE pathway;Ca2+ pathway;Beta-catenin independent WNT signaling;WNT ligand biogenesis and trafficking;GPCR signaling-G alpha i;Wnt Canonical;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.232
Intolerance Scores
- loftool
- 0.226
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 46.74
Haploinsufficiency Scores
- pHI
- 0.131
- hipred
- Y
- hipred_score
- 0.813
- ghis
- 0.477
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.532
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wnt11
- Phenotype
- craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; renal/urinary system phenotype; reproductive system 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- wnt11
- Affected structure
- cranial neural crest cell
- Phenotype tag
- abnormal
- Phenotype quality
- mislocalised ventrally
Gene ontology
- Biological process
- osteoblast differentiation;epithelial to mesenchymal transition;outflow tract morphogenesis;planar cell polarity pathway involved in axis elongation;protein phosphorylation;Wnt signaling pathway, calcium modulating pathway;positive regulation of gene expression;Wnt signaling pathway;neuron differentiation;bone mineralization;negative regulation of cell growth;adrenal gland development;positive regulation of cell migration;negative regulation of cell migration;response to nutrient levels;activation of protein kinase activity;positive regulation of transforming growth factor beta2 production;protein localization to cell surface;positive regulation of apoptotic process;negative regulation of apoptotic process;positive regulation of GTPase activity;cell fate commitment;maintenance of epithelial cell apical/basal polarity;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;paraxial mesoderm formation;notochord morphogenesis;embryonic skeletal system development;artery morphogenesis;positive regulation of stress fiber assembly;convergent extension involved in axis elongation;canonical Wnt signaling pathway;Wnt signaling pathway, planar cell polarity pathway;cloacal septation;ventricular septum morphogenesis;lung-associated mesenchyme development;negative regulation of cell death;ureteric bud morphogenesis;planar cell polarity pathway involved in gastrula mediolateral intercalation;negative regulation of cartilage development;somite development;neuroendocrine cell differentiation;secondary palate development;bicellular tight junction assembly;cellular response to mechanical stimulus;cellular response to retinoic acid;mesonephric duct development;negative regulation of mesenchymal cell proliferation;positive regulation of protein kinase C signaling;negative regulation of canonical Wnt signaling pathway;negative regulation of fibroblast growth factor production
- Cellular component
- extracellular region;extracellular space;cytoplasm;extracellular matrix
- Molecular function
- GTPase activator activity;frizzled binding;protein binding;protein kinase activator activity;transcription regulatory region DNA binding