SACM1L
Chr 3SAC1 like phosphatidylinositide phosphatase
Also known as: SAC1
The protein functions as a phosphoinositide phosphatase that hydrolyzes phosphatidylinositol 4-phosphate and other phosphoinositides, playing a critical role in cellular membrane organization. Mutations cause autosomal recessive developmental and epileptic encephalopathy with onset in infancy, characterized by severe intellectual disability, refractory seizures, and brain malformations. The gene shows high constraint against loss-of-function variants (LOEUF 0.37), consistent with its essential role in early development.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
ClinVar Variant Classifications
83 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 | 6 | 0 | 6 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 1 | 55 | 1 | 0 | 57 |
Likely Benign | 0 | 2 | 1 | 0 | 3 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 1 | 57 | 9 | 0 | 67 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SACM1L · 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