The Batten disease gene product CLN6 is a glycerophosphoglycerol epimerase that establishes S,S -BMP stereochemistry

Abstract Bis(monoacylglycero)phosphate (BMP), a lysosomal phospholipid essential for lipid catabolism and cholesterol clearance, has a noncanonical S,S glycerol configuration found in no other mammalian phospholipid, a feature necessary for its stability in the lysosome. How cells invert glycerol stereochemistry to build S,S -BMP has remained unexplained since this configuration was discovered five decades ago. Here, we show that the endoplasmic reticulum-resident Batten disease protein CLN6 is a Ca 2+ -dependent epimerase that isomerizes glycerophosphoglycerol (GPG) from R,S -GPG to S,S -GPG. CLN6-deficient cells, mouse tissues, and patient samples predominantly contain R,S -GPG, S,R -lysophosphatidylglycerol (LPG), and R,S -BMP instead of their S,S counterparts, with a net depletion of BMP. Purified CLN6 catalyzes GPG epimerization in vitro, an activity abolished by a pathogenic substitution in its substrate-binding pocket. Consistently, exogenous S,S -GPG restores BMP synthesis and relieves lipid storage in CLN6 -null cells. Our work establishes stereochemical commitment upstream of acylation, placing CLN6, CLN8, and CLN5 in sequence in BMP biosynthesis and unifying the lipid defect across these neurodegenerative disorders.