WNT10B
protein-codingWnt family member 10B, the group of Wnt family
Gene summary
The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It may be involved in breast cancer, and its protein signaling is likely a molecular switch that governs adipogenesis. This protein is 96% identical to the mouse Wnt10b protein at the amino acid level. This gene is clustered with another family member, WNT1, in the chromosome 12q13 region. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009157
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014901
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009157
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0014901
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014901
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009157
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0005486
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0016576
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009157
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Dental; Dermatologic; Musculoskeletal
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to WNT10B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003394.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 15 | 1 | 16 | |||
| missense | 2 | 6 | 81 | 7 | 3 | 99 |
| nonsense | 2 | 3 | 5 | |||
| start loss | 0 | |||||
| frameshift | 7 | 4 | 1 | 12 | ||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 11 | 15 | 82 | 22 | 4 | 134 |
Highest pathogenic variant AF is 0.000026244095
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003385.2 | 4 | MANE Select | |
| Ensembl | ENSP00000301061.4 | 4 | MANE Select | |
| Ensembl | ENSP00000385980.1 | 5 | Standard | |
| Ensembl | ENSP00000385980.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- G2/M transition of mitotic cell cycle
- negative regulation of transcription by RNA polymerase II
- chondrocyte differentiation
- lipid metabolic process
- cell cycle arrest
Molecular Function
- frizzled binding
- receptor ligand activity
Cellular Component
- extracellular region
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000301061
- Coding exons
- 4
- Length
- 6424
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 45
- Defined
- 125746
- p
- 0.000179
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.05 | 202 | 249 | 0.812 | 0.0000146 | 2490 |
| Missense (PolyPhen) | 84 | 102.25 | 0.82152 | 1075 | ||
| Synonymous | 0.950 | 87 | 99.0 | 0.879 | 0.00000495 | 826 |
| Loss of Function | 1.81 | 8 | 15.8 | 0.508 | 0.00000115 | 136 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00049 | 0.00049 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00018 | 0.00018 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Member of the Wnt ligand gene family that encodes for secreted proteins, which activate the Wnt signaling cascade. Specifically activates canonical Wnt/beta-catenin signaling and thus triggers beta-catenin/LEF/TCF-mediated transcriptional programs. Involved in signaling networks controlling stemness, pluripotency and cell fate decisions. Acts in the immune system, mammary gland, adipose tissue, bone and skin. {ECO:0000305|PubMed:16477437, ECO:0000305|PubMed:21447090, ECO:0000305|PubMed:27321946}.;
- Disease
- DISEASE: Split-hand/foot malformation 6 (SHFM6) [MIM:225300]: A limb malformation involving the central rays of the autopod and presenting with syndactyly, median clefts of the hands and feet, and aplasia and/or hypoplasia of the phalanges, metacarpals, and metatarsals. Some patients have been found to have mental retardation, ectodermal and craniofacial findings, and orofacial clefting. {ECO:0000269|PubMed:18515319}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tooth agenesis, selective, 8 (STHAG8) [MIM:617073]: A form of selective tooth agenesis, a common anomaly characterized by the congenital absence of one or more teeth. Selective tooth agenesis without associated systemic disorders has sometimes been divided into 2 types: oligodontia, defined as agenesis of 6 or more permanent teeth, and hypodontia, defined as agenesis of less than 6 teeth. The number in both cases does not include absence of third molars (wisdom teeth). STHAG8 inheritance is autosomal dominant. {ECO:0000269|PubMed:27321946}. Note=The disease is caused by mutations affecting the gene represented in this entry. Potential genotype-phenotype correlation between variants and the positions of missing teeth. {ECO:0000269|PubMed:27321946}.;
Recessive Scores
- pRec
- 0.217
Intolerance Scores
- LoFtool
- 0.764
- RVIS EVS
- -0.2
- RVIS percentile EVS
- 38.82
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.727
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |