RNA analysis of MYBPC3 splice-site variants reclassified variants from uncertain significance to likely pathogenic in 7% (4 of 56) of families with hypertrophic cardiomyopathy.
Cohort (n=557)
Does RNA analysis of MYBPC3 splice-site variants improve pathogenicity classification in patients with hypertrophic cardiomyopathy?
RNA analysis of MYBPC3 splice-site variants can confirm splicing errors and reclassify variants of uncertain significance to likely pathogenic, increasing the diagnostic yield in hypertrophic cardiomyopathy.
BACKGROUND: MYBPC3 splicing errors are a common cause of hypertrophic cardiomyopathy (HCM). Variants affecting essential splice-site dinucleotides inhibit splicing, whereas the impact of variants at conserved flanking nucleotides is less clear. We evaluated the contribution of MYBPC3 splice-site variants in a large cohort of patients with HCM and assessed the impact on splicing with RNA analysis. METHODS: Patients attending a specialized multidisciplinary clinic, with a clinical diagnosis of HCM and genetic testing of at least 46 cardiomyopathy-associated genes, were included. Patients with variants in MYBPC3 splice sites with in silico-predicted effects on splicing were selected. RNA was extracted from fresh venous blood or paraffin-embedded myocardial tissue of the patients, amplified, and sequenced. Variants were classified for pathogenicity using the American College of Medical Genetics and Genomics guidelines. RESULTS: We found 29 rare MYBPC3 splice-site variants in 56 of 557 (10%) unrelated HCM probands. Three variants were not predicted to alter RNA splicing, and 13 essential splice dinucleotide, nonsense, and short insertion or deletion variants were not further assessed. RNA analysis was performed on 9 variants (c.654+5G>C, c.772G>A, c.821+3G>T, c.927-9G>A, c.1090G>A, c.1624G>A, c.1624+4A>T, c.3190+5G>A, and c.3491-3C>G), and RNA splicing errors were confirmed for 7. Four variants in 4 families resulted in clinically meaningful reclassifications. CONCLUSIONS: After RNA analysis, 4 of 56 (7%) families with MYBPC3 splice-site variants were reclassified from uncertain clinical significance to likely pathogenic. RNA analysis of splice-site variants can assist in understanding pathogenicity and increase the diagnostic yield of genetic testing in HCM.
Singer et al. (Tue,) conducted a cohort in Hypertrophic cardiomyopathy (n=557). RNA analysis of MYBPC3 splice-site variants was evaluated on Reclassification of variant pathogenicity. RNA analysis of MYBPC3 splice-site variants reclassified variants from uncertain significance to likely pathogenic in 7% (4 of 56) of families with hypertrophic cardiomyopathy.