PIP4K2A
Chr 10phosphatidylinositol-5-phosphate 4-kinase type 2 alpha
Also known as: PI5P4KA, PIP5K2A, PIP5KII-alpha, PIP5KIIA, PIPK
This enzyme catalyzes the phosphorylation of phosphatidylinositol 5-phosphate to form phosphatidylinositol 4,5-bisphosphate, regulating phosphoinositide signaling pathways involved in autophagy, lysosome-peroxisome membrane contacts, and cellular lipid metabolism. Mutations cause neurodevelopmental disorders with intellectual disability and developmental delay, inherited in an autosomal recessive pattern. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.56), suggesting some tolerance to complete gene loss.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
ClinVar Variant Classifications
86 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 | 8 | 0 | 8 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 50 | 2 | 0 | 52 |
Likely Benign | 0 | 0 | 0 | 0 | 0 |
Benign | 0 | 1 | 3 | 2 | 6 |
| Total | 0 | 51 | 14 | 2 | 67 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PIP4K2A · 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