Cardiomyopathy is a genetic disorder of heart muscle; 2/3 of cases are gene-elusive
on panel testing. Cryptic splice site variants disrupt the normal pattern of mRNA
splicing through the creation of novel exon boundaries, resulting in abnormal protein
isoforms. These variants are not routinely evaluated during genetic testing in cardiomyopathy.
Our objective was to identify the contribution of cryptic splice site variants in
METHODS AND RESULTS
Cryptic splice site variants were identified using the SpliceAI software in whole
genome sequencing data from 231 unrelated pediatric cardiomyopathy probands enrolled
in the Heart Centre Biobank. Rare variants (gnomAD population allele frequency < 0.01%)
in cardiomyopathy genes were prioritized. RNAseq and proteomics data from available
matched myocardial samples were assessed for altered gene splicing and/or expression.
Eleven putatively pathogenic cryptic splice-altering variants were detected in 5%
of cases in CTNNA3, DSP, FHOD3, FKTN, FLNC, LDB3, MYBPC3, and VCL. FLNC:c.3791-1G>C,
FLNC:c.3790+5G>A, and CTNNA3:c.-6+12024G>A were validated in cases with available
tissue data (Figure 1). All three variants were associated with altered mRNA splicing
and reduced protein abundance.
Cryptic splice site variants may contribute to the genetics of cardiomyopathy through
altered mRNA splicing and reduced expression of disease genes. These findings highlight
the importance of searching not only for canonical splice site but also cryptic splice
site variants as part of the genetic evaluation of cardiomyopathy.