PNPLA6
Chr 19ARpatatin like domain 6, lysophospholipase
Also known as: BNHS, LNMS, NTE, NTEMND, OMCS, SPG39, iPLA2delta, sws
The protein is a phospholipase that deacetylates intracellular phosphatidylcholine to produce glycerophosphocholine and functions in neurite outgrowth and process elongation during neuronal differentiation from its location on the endoplasmic reticulum membrane. Mutations cause autosomal recessive disorders including spastic paraplegia 39, Boucher-Neuhauser syndrome, Oliver-McFarlane syndrome, and possibly Laurence-Moon syndrome. The pathogenic mechanism appears to involve gain-of-function effects.
Definitive — sufficient evidence for diagnostic panels
2 total gene-disease associations curated
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Highly missense-constrained (top ~0.1%)
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
PNPLA6 · 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