INPP1
Chr 2inositol polyphosphate-1-phosphatase
The protein is a magnesium-dependent phosphatase that hydrolyzes the 1-position phosphate from inositol 1,4-bisphosphate and inositol 1,3,4-trisphosphate, participating in inositol phosphate metabolism. Mutations cause pontocerebellar hypoplasia type 10, characterized by progressive microcephaly, severe developmental delay, seizures, and brain atrophy affecting the brainstem and cerebellum, with autosomal recessive inheritance. This gene is not highly constrained against loss-of-function variants.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Mild missense constraint
The highest-scoring mechanism for this gene is dominant-negative.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
100 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 | 27 | 0 | 27 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 1 | 50 | 1 | 0 | 52 |
Likely Benign | 0 | 5 | 0 | 0 | 5 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 1 | 55 | 29 | 1 | 86 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
INPP1 · 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