WNT2
Wnt family member 2, the group of Wnt family
Basic information
Region (hg38): 7:117275451-117323152
Previous symbols: [ "INT1L1" ]
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 WNT2 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 | |||||
| missense | 13 | 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 | 13 | 0 | 2 |
Variants in WNT2
This is a list of pathogenic ClinVar variants found in the WNT2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-117278181-T-C | Benign (Jun 06, 2018) | |||
| 7-117278241-C-T | not specified | Uncertain significance (May 10, 2022) | ||
| 7-117278279-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 7-117278283-T-C | not specified | Uncertain significance (Oct 05, 2023) | ||
| 7-117278301-A-G | not specified | Uncertain significance (Jun 22, 2024) | ||
| 7-117278325-C-T | not specified | Uncertain significance (Mar 22, 2022) | ||
| 7-117297673-C-T | Benign (Jun 13, 2018) | |||
| 7-117297734-A-G | not specified | Uncertain significance (Nov 03, 2022) | ||
| 7-117297776-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 7-117297862-G-T | not specified | Uncertain significance (Apr 30, 2024) | ||
| 7-117315142-C-A | not specified | Uncertain significance (Oct 25, 2023) | ||
| 7-117315153-C-T | not specified | Uncertain significance (Jul 12, 2022) | ||
| 7-117315241-T-C | not specified | Uncertain significance (Aug 17, 2021) | ||
| 7-117315342-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 7-117320668-G-A | not specified | Uncertain significance (Jun 02, 2024) | ||
| 7-117320674-C-G | not specified | Uncertain significance (Aug 12, 2022) | ||
| 7-117320677-T-C | not specified | Uncertain significance (Jun 05, 2024) | ||
| 7-117320690-G-A | not specified | Uncertain significance (May 30, 2023) | ||
| 7-117320716-A-G | not specified | Uncertain significance (Jun 07, 2024) | ||
| 7-117320789-T-C | not specified | Uncertain significance (Oct 13, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WNT2 | protein_coding | protein_coding | ENST00000265441 | 5 | 46659 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0178 | 0.978 | 125736 | 0 | 12 | 125748 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.18 | 172 | 222 | 0.776 | 0.0000130 | 2389 |
| Missense in Polyphen | 67 | 99.119 | 0.67595 | 1097 | ||
| Synonymous | -0.00704 | 85 | 84.9 | 1.00 | 0.00000514 | 687 |
| Loss of Function | 2.52 | 6 | 17.3 | 0.347 | 9.97e-7 | 171 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000579 | 0.0000579 |
| Ashkenazi Jewish | 0.0000994 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000563 | 0.0000462 |
| European (Non-Finnish) | 0.0000534 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family (PubMed:20018874). Functions as upstream regulator of FGF10 expression. Plays an important role in embryonic lung development. May contribute to embryonic brain development by regulating the proliferation of dopaminergic precursors and neurons (By similarity). {ECO:0000250|UniProtKB:P21552, ECO:0000269|PubMed:20018874}.;
- 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);WNT-Core;Differentiation Pathway;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;Wnt Canonical;Wnt signaling network;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.435
Intolerance Scores
- loftool
- 0.577
- rvis_EVS
- -0.2
- rvis_percentile_EVS
- 38.82
Haploinsufficiency Scores
- pHI
- 0.140
- hipred
- Y
- hipred_score
- 0.792
- ghis
- 0.517
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.996
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wnt2
- Phenotype
- respiratory system phenotype; embryo phenotype; growth/size/body region phenotype; 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); 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); homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- wnt2
- Affected structure
- pancreatic B cell
- Phenotype tag
- abnormal
- Phenotype quality
- mislocalised
Gene ontology
- Biological process
- positive regulation of endothelial cell proliferation;positive regulation of mesenchymal cell proliferation;lens development in camera-type eye;cell-cell signaling;positive regulation of cell population proliferation;regulation of signaling receptor activity;Wnt signaling pathway;neurogenesis;neuron differentiation;lung development;cell proliferation in midbrain;cell fate commitment;positive regulation of transcription by RNA polymerase II;positive regulation of fibroblast proliferation;positive regulation of DNA-binding transcription factor activity;atrial cardiac muscle tissue morphogenesis;positive regulation of cardiac muscle cell proliferation;canonical Wnt signaling pathway;cardiac epithelial to mesenchymal transition;lung induction;positive regulation of epithelial cell proliferation involved in lung morphogenesis;labyrinthine layer blood vessel development;iris morphogenesis;mammary gland epithelium development;cellular response to retinoic acid;cellular response to transforming growth factor beta stimulus;midbrain dopaminergic neuron differentiation;canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
- Cellular component
- extracellular region;extracellular space;cytoplasm;extrinsic component of external side of plasma membrane;collagen-containing extracellular matrix;Wnt signalosome
- Molecular function
- frizzled binding;cytokine activity;protein binding;receptor ligand activity