GDE1
Chr 16glycerophosphodiester phosphodiesterase 1
Also known as: 363E6.2, MIR16
This glycerophosphodiester phosphodiesterase hydrolyzes glycerophosphodiesters and participates in bioactive N-acylethanolamine biosynthesis including anandamide, with the gene showing low constraint to loss-of-function variants (pLI near 0). Biallelic pathogenic variants cause autosomal recessive spastic paraplegia with intellectual disability and seizures, typically with childhood onset. The condition primarily affects the central nervous system with progressive spasticity and developmental delays.
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
70 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 | 15 | 0 | 15 |
Likely Pathogenic | 0 | 0 | 0 | 0 | 0 |
VUS | 0 | 40 | 4 | 0 | 44 |
Likely Benign | 0 | 0 | 0 | 0 | 0 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 40 | 19 | 1 | 60 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
GDE1 · 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