PLA2G10
Chr 16phospholipase A2 group X
Also known as: GXPLA2, GXSPLA2, SPLA2, sPLA2-X
The protein is a secretory calcium-dependent phospholipase A2 that hydrolyzes phospholipids to release fatty acids and lysophospholipids, playing key roles in lipid metabolism, inflammation, gut epithelial function, and antimicrobial defense. Mutations cause autosomal recessive benign recurrent intrahepatic cholestasis type 2, a liver disorder characterized by episodic cholestasis with pruritus and jaundice. The gene shows tolerance to loss-of-function variation, consistent with the recessive inheritance pattern of associated disease.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function 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
49 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 | 20 | 0 | 20 |
Likely Pathogenic | 0 | 0 | 5 | 0 | 5 |
VUS | 0 | 7 | 13 | 0 | 20 |
Likely Benign | 0 | 1 | 1 | 1 | 3 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 8 | 39 | 1 | 48 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PLA2G10 · 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