WNT3
Wnt family member 3, the group of Wnt family
Basic information
Region (hg38): 17:46762506-46833154
Previous symbols: [ "INT4" ]
Links
Phenotypes
GenCC
Source:
- tetraamelia syndrome 1 (Moderate), mode of inheritance: AR
- tetraamelia syndrome 1 (Definitive), mode of inheritance: AR
- tetraamelia-multiple malformations syndrome (Supportive), mode of inheritance: AR
- tetraamelia syndrome 1 (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Tetraamelia syndrome 1 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Renal | 14872406 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (102 variants)
- not_specified (23 variants)
- WNT3-related_disorder (3 variants)
- Bladder_exstrophy-epispadias-cloacal_extrophy_complex (2 variants)
- Tetraamelia_syndrome_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030753.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 36 | 38 | ||||
| missense | 46 | 47 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 1 | 47 | 36 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WNT3 | protein_coding | protein_coding | ENST00000225512 | 4 | 70649 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.875 | 0.125 | 122322 | 0 | 1 | 122323 | 0.00000409 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.18 | 109 | 251 | 0.435 | 0.0000184 | 2313 |
| Missense in Polyphen | 30 | 99.567 | 0.3013 | 918 | ||
| Synonymous | 0.595 | 106 | 114 | 0.929 | 0.00000937 | 706 |
| Loss of Function | 3.19 | 2 | 15.6 | 0.128 | 7.59e-7 | 157 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000203 | 0.000101 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| 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:26902720). Required for normal gastrulation, formation of the primitive streak, and for the formation of the mesoderm during early embryogenesis. Required for normal formation of the apical ectodermal ridge (By similarity). Required for normal embryonic development, and especially for limb development (PubMed:14872406). {ECO:0000250|UniProtKB:P17553, ECO:0000269|PubMed:14872406, ECO:0000269|PubMed:26902720, ECO:0000305}.;
- Disease
- DISEASE: Tetraamelia syndrome 1 (TETAMS1) [MIM:273395]: A form of tetraamelia, a rare disease characterized by rudimentary appendages or complete absence of all four limbs, and other anomalies such as craniofacial, nervous system, pulmonary, skeletal and urogenital defects. TETAMS1 patients manifest complete limb agenesis without defects of scapulae or clavicles. Other features include bilateral cleft lip/palate, diaphragmatic defect with bilobar right lung, renal and adrenal agenesis, pelvic hypoplasia, and urogenital defects. TETAMS1 transmission pattern is consistent with autosomal recessive inheritance. {ECO:0000269|PubMed:14872406}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- 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);Endoderm Differentiation;Mesodermal Commitment Pathway;EDA Signalling in Hair Follicle Development;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;TCF dependent signaling in response to WNT;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.270
Intolerance Scores
- loftool
- 0.0728
- rvis_EVS
- -0.45
- rvis_percentile_EVS
- 24
Haploinsufficiency Scores
- pHI
- 0.547
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wnt3
- Phenotype
- growth/size/body region phenotype; cellular phenotype; embryo phenotype; normal 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; limbs/digits/tail phenotype;
Zebrafish Information Network
- Gene name
- wnt3
- Affected structure
- cloaca
- Phenotype tag
- abnormal
- Phenotype quality
- increased width
Gene ontology
- Biological process
- cell morphogenesis;mesoderm formation;gamete generation;axon guidance;anterior/posterior axis specification;dorsal/ventral axis specification;regulation of signaling receptor activity;positive regulation of gene expression;Wnt signaling pathway;positive regulation of Wnt signaling pathway;neuron differentiation;embryonic forelimb morphogenesis;embryonic hindlimb morphogenesis;canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation;canonical Wnt signaling pathway involved in osteoblast differentiation;cell fate commitment;positive regulation of collateral sprouting in absence of injury;negative regulation of axon extension involved in axon guidance;regulation of neurogenesis;Spemann organizer formation at the anterior end of the primitive streak;canonical Wnt signaling pathway;limb bud formation;head morphogenesis;mammary gland epithelium development;cellular response to retinoic acid;stem cell proliferation;canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation;canonical Wnt signaling pathway involved in stem cell proliferation
- Cellular component
- extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi lumen;plasma membrane;endocytic vesicle membrane;extracellular matrix;extracellular exosome;Wnt signalosome
- Molecular function
- frizzled binding;protein binding;protein domain specific binding;receptor ligand activity