LDLR Variant Classification Through Activity-Normalized Prime Editing Screening.

Activity-normalized prime editing screening of 5184 LDLR coding variants yields functional scores that robustly separate pathogenic from benign ClinVar variants and align with UK Biobank LDL-C.

• Why it matters: Most LDLR variants lack clinical classification, leaving patients without actionable guidance for lipid-lowering therapy and cascade testing of at-risk relatives.
• What they did: The pipeline pairs each prime editing guide RNA with a genotypic outcome reporter to correct variable editing efficiency, then jointly analyzes all missense variants at each amino acid position. It correlates reporter prime editing with endogenous variant installation frequency and calibrates functional evidence to ACMG/AMP.
• The result: Using integrated evidence, 322 of 434 LDLR variants of uncertain significance, conflicting, or absent from ClinVar meet reclassification thresholds for expert review, and the screen identifies gain-of-function clusters and splice-altering variants missed by cDNA-based screens.