Identification of pathogenic gene mutations in LMNA and MYBPC3 that alter RNA splicing

Significance Sequence variants that create or eliminate splice sites are often clinically classified as variants of unknown significance (VUS) due to imperfect understanding of RNA splice signals and cumbersome functional assays. In autosomal dominant disorders caused by haploinsufficiency, variants that alter normal splicing of one allele are pathogenic. We developed enhanced computational tools to prioritize potential splice-altering VUS and used a minigene assay to functionally confirm splice-altering sequence variants. In studying all reported variants across LMNA and MYBPC3 , two known heart disease genes, we demonstrate that ∼5% of VUS from affected patients alter splicing and are undetected disease-causing variants. This strategy improves clinical detection of pathogenic variants and should be broadly relevant to other human disorders that are caused by haploinsufficiency.