SPART
Chr 13ARspartin
Also known as: SPG20, TAHCCP1
The encoded protein functions as a lipophagy receptor that regulates lipid droplet turnover in motor neurons and serves as a lipid transfer protein, while also participating in endosomal trafficking and cytokinesis. Mutations cause Troyer syndrome, an autosomal recessive spastic paraplegia characterized by spasticity and neurological dysfunction. This gene shows low constraint against loss-of-function variants (LOEUF 0.838), consistent with its recessive inheritance pattern where biallelic mutations are required for disease manifestation.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
The highest-scoring mechanism for this gene is gain-of-function.
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
472 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 | 16 | 0 | 50 | 0 | 66 |
Likely Pathogenic | 11 | 1 | 1 | 0 | 13 |
VUS | 6 | 183 | 45 | 5 | 239 |
Likely Benign | 1 | 6 | 37 | 71 | 115 |
Benign | 0 | 0 | 13 | 1 | 14 |
Conflicting | — | 16 | |||
| Total | 34 | 190 | 146 | 77 | 463 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SPART · 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