WNT3A
Wnt family member 3A, the group of Wnt family
Basic information
Region (hg38): 1:228006998-228061271
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 WNT3A 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 | 35 | 37 | ||||
| missense | 64 | 66 | ||||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 14 | 16 | ||||
| Total | 0 | 0 | 67 | 49 | 6 |
Variants in WNT3A
This is a list of pathogenic ClinVar variants found in the WNT3A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-228007139-T-C | Uncertain significance (Jan 02, 2022) | |||
| 1-228007140-C-T | Likely benign (Oct 17, 2023) | |||
| 1-228007153-C-T | Uncertain significance (Feb 14, 2023) | |||
| 1-228007155-C-G | Likely benign (May 16, 2023) | |||
| 1-228007178-T-C | Uncertain significance (Sep 04, 2022) | |||
| 1-228007184-G-A | not specified | Uncertain significance (Jun 06, 2022) | ||
| 1-228007191-G-A | Likely benign (Jun 04, 2022) | |||
| 1-228007215-C-G | Likely benign (Mar 17, 2023) | |||
| 1-228022648-C-T | Benign (Jul 12, 2023) | |||
| 1-228022649-G-A | Likely benign (Jul 31, 2023) | |||
| 1-228022670-G-A | Likely benign (Mar 03, 2022) | |||
| 1-228022683-C-T | Uncertain significance (Oct 23, 2022) | |||
| 1-228022697-C-A | Likely benign (Jun 26, 2023) | |||
| 1-228022706-G-A | Likely benign (May 20, 2023) | |||
| 1-228022747-A-G | Uncertain significance (Feb 21, 2023) | |||
| 1-228022773-G-A | not specified | Uncertain significance (May 17, 2023) | ||
| 1-228022781-C-G | not specified | Uncertain significance (Feb 27, 2024) | ||
| 1-228022787-C-A | Likely benign (Jun 17, 2023) | |||
| 1-228022791-G-T | Uncertain significance (Aug 26, 2021) | |||
| 1-228022797-G-A | Uncertain significance (Dec 07, 2023) | |||
| 1-228022810-T-G | Uncertain significance (Nov 04, 2023) | |||
| 1-228022821-G-T | Uncertain significance (Nov 06, 2023) | |||
| 1-228022823-G-A | Likely benign (Jan 22, 2024) | |||
| 1-228022838-C-A | Uncertain significance (Dec 24, 2022) | |||
| 1-228022839-C-T | Uncertain significance (Jul 24, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WNT3A | protein_coding | protein_coding | ENST00000284523 | 4 | 54210 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.965 | 0.0351 | 125637 | 0 | 3 | 125640 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.00 | 160 | 249 | 0.643 | 0.0000170 | 2275 |
| Missense in Polyphen | 53 | 113.54 | 0.46681 | 1018 | ||
| Synonymous | 2.41 | 79 | 111 | 0.709 | 0.00000842 | 699 |
| Loss of Function | 3.33 | 1 | 14.8 | 0.0675 | 6.35e-7 | 156 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000202 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors (Probable). Functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family (PubMed:20093360, PubMed:21244856, PubMed:24841207, PubMed:26902720). Required for normal embryonic mesoderm development and formation of caudal somites. Required for normal morphogenesis of the developing neural tube (By similarity). Mediates self-renewal of the stem cells at the bottom on intestinal crypts (in vitro) (PubMed:26902720). {ECO:0000250|UniProtKB:P27467, ECO:0000269|PubMed:20093360, ECO:0000269|PubMed:21244856, ECO:0000269|PubMed:24841207, ECO:0000269|PubMed:26902720, ECO:0000305}.;
- 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);MicroRNAs 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;MicroRNAs in cardiomyocyte hypertrophy;Regulation of Microtubule Cytoskeleton;Neural Crest Differentiation;Cardiac Progenitor Differentiation;Differentiation Pathway;Gene regulatory network modelling somitogenesis;Mesodermal Commitment Pathway;Extracellular vesicle-mediated signaling in recipient cells;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;Disassembly of the destruction complex and recruitment of AXIN to the membrane;Regulation of FZD by ubiquitination;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;Negative regulation of TCF-dependent signaling by WNT ligand antagonists;WNT ligand biogenesis and trafficking;GPCR signaling-G alpha i;Wnt;Wnt Canonical;Wnt signaling network;Degradation of beta catenin;TCF dependent signaling in response to WNT;Canonical Wnt signaling pathway;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.585
Intolerance Scores
- loftool
- 0.276
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.58
Haploinsufficiency Scores
- pHI
- 0.149
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.498
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.921
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wnt3a
- Phenotype
- hearing/vestibular/ear 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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; 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); craniofacial phenotype; muscle phenotype;
Zebrafish Information Network
- Gene name
- wnt3a
- Affected structure
- aortic arch
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- osteoblast differentiation;in utero embryonic development;positive regulation of cytokine production;positive regulation of protein phosphorylation;heart looping;positive regulation of receptor internalization;negative regulation of heart induction by canonical Wnt signaling pathway;axon guidance;cell population proliferation;positive regulation of cell population proliferation;COP9 signalosome assembly;regulation of signaling receptor activity;positive regulation of gene expression;negative regulation of neuron projection development;Wnt signaling pathway;spinal cord association neuron differentiation;hippocampus development;cell proliferation in forebrain;Wnt signaling pathway involved in forebrain neuroblast division;dorsal/ventral neural tube patterning;hemopoiesis;neuron differentiation;extracellular matrix organization;mammary gland development;positive regulation of B cell proliferation;positive regulation of protein binding;positive regulation of peptidyl-serine phosphorylation;cell proliferation in midbrain;cellular protein localization;skeletal muscle cell differentiation;post-anal tail morphogenesis;synaptic vesicle recycling;inner ear morphogenesis;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;cell fate commitment;negative regulation of fat cell differentiation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of mesodermal cell fate specification;paraxial mesodermal cell fate commitment;positive regulation of skeletal muscle tissue development;positive regulation of collateral sprouting in absence of injury;negative regulation of axon extension involved in axon guidance;negative regulation of neurogenesis;modulation of chemical synaptic transmission;regulation of synapse organization;positive regulation of DNA-binding transcription factor activity;canonical Wnt signaling pathway;positive regulation of protein tyrosine kinase activity;positive regulation of dermatome development;canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment;secondary palate development;regulation of microtubule cytoskeleton organization;platelet aggregation;cellular response to retinoic acid;axis elongation involved in somitogenesis;positive regulation of canonical Wnt signaling pathway;calcium ion transmembrane transport via low voltage-gated calcium channel;presynapse assembly;postsynapse to nucleus signaling pathway;negative regulation of neuron death;positive regulation of protein localization to plasma membrane;negative regulation of dopaminergic neuron differentiation;positive regulation of core promoter binding;beta-catenin destruction complex disassembly;Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation;regulation of presynapse assembly;positive regulation of cell-cell adhesion mediated by cadherin;positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation;positive regulation of neural precursor cell proliferation;positive regulation of hepatocyte proliferation;positive regulation of cardiac muscle cell differentiation
- Cellular component
- extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi lumen;plasma membrane;cell surface;endocytic vesicle membrane;early endosome membrane;extracellular exosome;presynapse;glutamatergic synapse;Wnt-Frizzled-LRP5/6 complex
- Molecular function
- transcription coactivator activity;signaling receptor binding;frizzled binding;protein binding;protein domain specific binding;co-receptor binding;receptor ligand activity