VANGL2

Chr 1

VANGL planar cell polarity protein 2

Also known as: LPP1, LTAP, STB1, STBM, STBM1

NCBI Gene: 57216ENSG00000162738UniProt: Q9ULK5

The protein encoded by this gene is a membrane protein involved in the regulation of planar cell polarity, especially in the stereociliary bundles of the cochlea. The encoded protein transmits directional signals to individual cells or groups of cells in epithelial sheets. This protein is also involved in the development of the neural plate. [provided by RefSeq, Sep 2011]

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtNeural tube defects

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
3
Active trials
38
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.39
LOEUF
Multiple*
Mechanism· predicted
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.39LOEUF
pLI 0.843
Z-score 3.75
OE 0.17 (0.08–0.39)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.43Z-score
OE missense 0.78 (0.70–0.86)
253 obs / 325.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.17 (0.08–0.39)
0≤0.351.4
Missense OE?0.78 (0.70–0.86)
0≤0.61.4
Synonymous OE?1.00
0≤1.21.6
LoF obs/exp: 4 / 23.7Missense obs/exp: 253 / 325.8Syn Z: 0.00

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

VANGL2 · protein map & ClinVar variants

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

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients