PIGY
Chr 4ARphosphatidylinositol glycan anchor biosynthesis class Y
Also known as: HPMRS6, PIG-Y
The protein encoded by PIGY is part of the GPI-N-acetylglucosaminyltransferase complex that initiates glycosylphosphatidylinositol (GPI) biosynthesis in the endoplasmic reticulum, where GPI serves as an anchor for many surface proteins involved in cell-cell interactions. Mutations cause hyperphosphatasia with impaired intellectual development syndrome 6 through an autosomal recessive inheritance pattern. The pathogenic mechanism involves gain-of-function mutations.
Limited evidence — not for standalone diagnostic reporting
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
46 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 1 | 1 | 24 | 0 | 26 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 12 | 0 | 0 | 12 |
Likely Benign | 0 | 2 | 0 | 2 | 4 |
Benign | 0 | 0 | 2 | 1 | 3 |
| Total | 1 | 15 | 27 | 3 | 46 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PIGY · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools