WNT10B

protein-coding

Wnt 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

NM_003394.4

Inheritance

AR, AD

ClinVar variants

P:26U:82B:26

Top phenotype

Tooth agenesis, selective, 8; Split-hand/foot malformation 6

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr12:48,965,340-48,971,735

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~6.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

split hand-foot malformation 6MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0009157

Submitter: Ambry Genetics

tooth agenesis, selective, 8LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014901

Submitter: Labcorp Genetics (formerly Invitae)

split hand-foot malformation 6STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009157

Submitter: Labcorp Genetics (formerly Invitae)

tooth agenesis, selective, 8MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0014901

Submitter: Ambry Genetics

tooth agenesis, selective, 8STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014901

Submitter: PanelApp Australia

split hand-foot malformation 6DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009157

Submitter: G2P

tooth agenesisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0005486

Submitter: Orphanet

split hand-foot malformationSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016576

Submitter: Orphanet

split hand-foot malformation 6STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009157

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Tooth agenesis, selective, 8; Split-hand/foot malformation 6AD/AR

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

Refs: 12072797; 18515319; 20635353; 21554266; 27321946; 29427788Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WNT10B variants in ClinVar

6 Conditions Cataloged
Inborn genetic diseasesTotal: 63
not providedTotal: 60
Split hand-foot malformation 6Total: 26
WNT10B-related disorderTotal: 10
not specifiedTotal: 6
Tooth agenesis, selective, 8Total: 5

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.

EffectPLPVUSLBBSum
synonymous
15
clinvar
1
clinvar
16
missense
2
clinvar
6
clinvar
81
clinvar
7
clinvar
3
clinvar
99
nonsense
2
clinvar
3
clinvar
5
start loss
0
frameshift
7
clinvar
4
clinvar
1
clinvar
12
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total111582224134

Highest pathogenic variant AF is 0.000026244095

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003394.4RefSeqNP_003385.24MANE Select
ENST00000301061.9EnsemblENSP00000301061.44MANE Select
ENST00000403957.5EnsemblENSP00000385980.15Standard
ENST00000403957.6EnsemblENSP00000385980.15Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.052022490.8120.00001462490
Missense (PolyPhen)84102.250.821521075
Synonymous0.9508799.00.8790.00000495826
Loss of Function1.81815.80.5080.00000115136

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.000290.00029rare
Ashkenazi Jewish00.0absent
East Asian0.000490.00049rare
Finnish00.0absent
European (Non-Finnish)0.000180.00018rare
South Asian0.0000980.000098rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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