Single antisense oligonucleotides correct diverse splicing mutations in hotspot exons

Mutations that impact splicing play a significant role in disease etiology but are not fully understood. To characterize the impact of exonic variants on splicing in 71 clinically actionable disease genes in asymptomatic people, we analyzed 32,112 exonic mutations from ClinVar and Geisinger MyCode using a minigene reporter assay. We identify 1,733 splice-disrupting mutations, with the most extreme variants likely being deleterious. We report that these variants are not distributed evenly across exons but are mostly concentrated in the ~8% of exons that are most susceptible to splicing mutations (i.e., hotspot exons). We demonstrate how multiple, splice-disrupting mutations in these exons can be reverted by the same ASOs targeting the splice sites of either their upstream or downstream flanking exons. This finding supports the feasibility of developing single therapeutic ASOs that could revert all splice-altering variants localized to a particular exon.