WNT7B

Chr 22

Wnt family member 7B

NCBI Gene: 7477ENSG00000188064UniProt: P56706

This gene is a member of the WNT gene family, which consists of structurally related genes that 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. Among members of the human WNT family, this gene product is most similar to WNT7A protein. [provided by RefSeq, Oct 2008]

141
ClinVar variants
84
Pathogenic / LP
0.00
pLI score
1
Active trials
Clinical Summary— WNT7B
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
84 Pathogenic / Likely Pathogenic· 44 VUS of 141 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.82LOEUF
pLI 0.001
Z-score 2.12
OE 0.45 (0.27–0.82)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.99Z-score
OE missense 0.65 (0.58–0.74)
171 obs / 261.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.45 (0.27–0.82)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.65 (0.58–0.74)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.24
0≤1.21.6
LoF obs/exp: 8 / 17.6Missense obs/exp: 171 / 261.7Syn Z: -2.02

ClinVar Variant Classifications

141 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic80
Likely Pathogenic4
VUS44
Likely Benign4
Benign3
80
Pathogenic
4
Likely Pathogenic
44
VUS
4
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
1
79
0
80
Likely Pathogenic
1
1
2
0
4
VUS
0
40
4
0
44
Likely Benign
0
0
0
4
4
Benign
0
0
1
2
3
Total142866135

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

WNT7B · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

WNT7B-related PDAC syndrome

moderate
ARUndeterminedAbsent Gene Product, Altered Gene Product Structure, Decreased Gene Product Level
Dev. Disorders
G2P ↗
missense variantstop gained NMD triggering

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Endometrial Assembloid Model Reveals Endometrial Gland Development Regulation by Estradiol-Driven WNT7B Suppression.
Li X et al.·Adv Sci (Weinh)
2026Functional
Epithelial WNT secretion drives niche escape of developing gastric cancer.
Lee J et al.·Mol Cancer
2025
H2BC9 lactylation modulates esophageal squamous cell carcinoma progression via the Wnt/β-catenin signaling pathway.
Zhang Y et al.·J Transl Med
2025
A founder variant expands the phenotype of WNT7B-related PDAC syndrome.
AlAbdi L et al.·Clin Genet
2024Case report
State of the Science for Kidney Disorders in Phelan-McDermid Syndrome: UPK3A, FBLN1, WNT7B, and CELSR1 as Candidate Genes.
McCoy MD et al.·Genes (Basel)
2022Review
ZNF831-YTHDF1-DNMT1/3a feedback loop regulates lung carcinogenesis and progression through WNT7B-FZD5-β-catenin signalling axis.
Chen D et al.·Free Radic Biol Med
2025
The miR-34a/WNT7B modulates the sensitivity of cholangiocarcinoma cells to p53-mediated photodynamic therapy toxicity.
Han Y et al.·Biochem Biophys Res Commun
2022
WNT7B promotes bone formation in part through mTORC1.
Chen J et al.·PLoS Genet
2014
WNT7B promotes cancer progression via WNT/β-catenin signaling pathway and predicts a poor prognosis in oral squamous cell carcinoma.
Li Y et al.·BMC Oral Health
2024
Four Pharmacogenomic Variants Strongly Linked to Corticosteroid-Induced Avascular Necrosis in Children with Cancer.
Cordova-Delgado M et al.·J Clin Pharmacol
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Proven Pathogenic or Probably Pathogenic TBR1 Variant

A Pilot, Multicentre, Controlled, Open-label Study Evaluating 24 Months of Lithium Carbonate Treatment in Patients With TBR1-related Neurocognitive Disorder

RECRUITING
NCT06776848Phase PHASE1, PHASE2Centre Hospitalier Universitaire DijonStarted 2025-09-12
Observation phaseLithium treatmentbiological monitoring

External Resources

Links to major genomics databases and tools