PHLPP1
Chr 18PH domain and leucine rich repeat protein phosphatase 1
Also known as: PHLPP, PLEKHE1, PPM3A, SCOP
This gene encodes a serine/threonine protein phosphatase that regulates cell survival and apoptosis by dephosphorylating AKT, protein kinase C, and other signaling proteins involved in neuronal function and memory formation. Mutations cause autosomal dominant intellectual disability with seizures and behavioral abnormalities, typically presenting in early childhood. The gene is highly constrained against loss-of-function mutations, indicating that proper dosage is critical for normal neurodevelopment.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Mild missense constraint
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
300 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 | 54 | 0 | 54 |
Likely Pathogenic | 0 | 0 | 5 | 0 | 5 |
VUS | 0 | 206 | 4 | 0 | 210 |
Likely Benign | 0 | 7 | 1 | 0 | 8 |
Benign | 0 | 1 | 1 | 2 | 4 |
| Total | 0 | 214 | 65 | 2 | 281 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PHLPP1 · 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
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