PYGO2

Chr 1

pygopus family PHD finger 2

Also known as: 1190004M21Rik

NCBI Gene: 90780ENSG00000163348UniProt: Q9BRQ0OMIM: 606903

Predicted to enable chromatin binding activity; histone acetyltransferase regulator activity; and histone binding activity. Predicted to be involved in Wnt signaling pathway. Predicted to act upstream of or within several processes, including canonical Wnt signaling pathway; lens development in camera-type eye; and spermatid nucleus differentiation. Located in nucleoplasm. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Jun 2026]

OMIMResearchGenerating clinical summary…

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.
0
Active trials
10
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.28
LOEUF· LoF intol.
LOF
Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.28LOEUF
pLI 0.967
Z-score 3.01
OE 0.00 (0.00–0.28)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
1.10Z-score
OE missense 0.78 (0.69–0.89)
161 obs / 205.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.00 (0.00–0.28)
0≤0.351.4
Missense OE?0.78 (0.69–0.89)
0≤0.61.4
Synonymous OE?1.12
0≤1.21.6
LoF obs/exp: 0 / 10.6Missense obs/exp: 161 / 205.4Syn Z: -0.86

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PYGO2 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

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