PGAP3
Chr 17ARpost-GPI attachment to proteins phospholipase 3
Also known as: AGLA546, CAB2, PERLD1, PP1498, hCOS16
This gene encodes a GPI-specific phospholipase that removes unsaturated fatty acids from GPI anchors in the Golgi apparatus, which is critical for proper integration of GPI-anchored proteins into lipid rafts. Mutations cause hyperphosphatasia with impaired intellectual development syndrome 4, an autosomal recessive disorder characterized by cognitive disability and elevated alkaline phosphatase levels. The gene shows tolerance to loss-of-function variants (pLI 0.002, LOEUF 0.83), consistent with its recessive inheritance pattern.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
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
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
PGAP3 · 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