Mutations in ciliary genes cause a spectrum of both overlapping and distinct clinical syndromes (ciliopathies). CEP120 and CC2D2A are paradigmatic examples for this genetic heterogeneity and pleiotropy as mutations in both cause Joubert syndrome but are also associated with skeletal ciliopathies and Meckel syndrome, respectively. The molecular basis for this phenotypical variability is not understood but basal exon skipping likely contributes to tolerance for deleterious mutations via preservation of the amount of expressed functional protein. Here we systematically review and annotate genetic variants described in CEP120- and CC2D2A-associated disease and confirm more severe clinical presentations with biallelic truncating CC2D2A mutations. Combining in silico and ex vivo studies, we identify alternative basal exon skipping in the kidney, with possible relevance for organ-specific disease manifestations. Finally, we propose a multimodal approach to classify exons amenable to exon skipping and by mapping reported variants, 14 truncating mutations in 7 CC2D2A exons were identified as potentially rescuable by targeted exon skipping, an approach that is already in clinical use for other inherited human diseases. We conclude that genotype-phenotype correlations for CC2D2A support the deleteriousness of null alleles and that CC2D2A, but not CEP120, offers potential for therapeutic exon skipping approaches.