SCP2
Chr 1ARsterol carrier protein 2
Also known as: NLTP, NSL-TP, SCOX, SCP-2, SCP-CHI, SCP-X, SCPX, nsLTP
This gene encodes sterol carrier protein X (SCPx), a peroxisome-associated thiolase involved in branched chain fatty acid oxidation, and sterol carrier protein 2 (SCP2), an intracellular lipid transfer protein. Mutations cause leukoencephalopathy with dystonia and motor neuropathy with autosomal recessive inheritance. The gene is highly constrained against loss-of-function variants (LOEUF 0.76) and is highly expressed in organs involved in lipid metabolism.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
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
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
SCP2 · 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
External Resources
Links to major genomics databases and tools