PGAP4
Chr 9post-GPI attachment to proteins GalNAc transferase 4
Also known as: C9orf125, TMEM246
PGAP4 encodes a Golgi-resident glycosyltransferase that catalyzes N-acetylgalactosamine transfer to the first mannose of glycosylphosphatidylinositol (GPI) anchors during GPI-anchor maturation. Mutations cause autosomal recessive intellectual disability with seizures, abnormal gait, and delayed speech development. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.696), and patients typically present in early childhood with developmental delays and neurological symptoms.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
ClinVar Variant Classifications
95 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 | 0 | 0 | 32 | 0 | 32 |
Likely Pathogenic | 0 | 0 | 2 | 0 | 2 |
VUS | 0 | 52 | 3 | 0 | 55 |
Likely Benign | 0 | 0 | 0 | 0 | 0 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 52 | 37 | 0 | 89 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PGAP4 · 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 →No open access results found
External Resources
Links to major genomics databases and tools