Spatial and Functional Distribution of MYBPC3 Pathogenic Variants and Clinical Outcomes in Patients With Hypertrophic Cardiomyopathy

Abstract

Background - Pathogenic variants in MYBPC3 , encoding cardiac MyBP-C, are the most common cause of familial hypertrophic cardiomyopathy. A large number of unique MYBPC3 variants and relatively small genotyped HCM cohorts have precluded detailed genotype-phenotype correlations. Methods - Patients with HCM and MYBPC3 variants were identified from the Sarcomeric Human Cardiomyopathy Registry (SHaRe). Variant types and locations were analyzed, morphologic severity was assessed, and time-event analysis was performed (composite clinical outcome of sudden death, class III/IV heart failure, LVAD/transplant, atrial fibrillation). For selected missense variants falling in enriched domains, myofilament localization and degradation rates were measured in vitro . Results - Among 4,756 genotyped HCM patients in SHaRe, 1,316 patients were identified with adjudicated pathogenic truncating (N=234 unique variants, 1047 patients) or non-truncating (N=22 unique variants, 191 patients) variants in MYBPC3 . Truncating variants were evenly dispersed throughout the gene, and hypertrophy severity and outcomes were not associated with variant location (grouped by 5' - 3' quartiles or by founder variant subgroup). Non-truncating pathogenic variants clustered in the C3, C6, and C10 domains (18 of 22, 82%, p<0.001 vs. gnomAD common variants) and were associated with similar hypertrophy severity and adverse event rates as observed with truncating variants. MyBP-C with variants in the C3, C6, and C10 domains was expressed in rat ventricular myocytes. C10 mutant MyBP-C failed to incorporate into myofilaments and degradation rates were accelerated by ~90%, while C3 and C6 mutant MyBP-C incorporated normally with degradation rate similar to wild-type. Conclusions - Truncating variants account for 91% of MYBPC3 pathogenic variants and cause similar clinical severity and outcomes regardless of location, consistent with locus-independent loss-of-function. Non-truncating MYBPC3 pathogenic variants are regionally clustered, and a subset also cause loss-of-function through failure of myofilament incorporation and rapid degradation. Cardiac morphology and clinical outcomes are similar in patients with truncating vs. non-truncating variants.

Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation

“…Inclusion criteria included a site-designated diagnosis of HCM using standard diagnostic criteria. 8 SHaRe nontruncating MYBPC3 missense variants (Tables S1, S2) were classified as previously reported 14 in accordance with American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) joint guidelines, leveraging available clinical and experimental data. 3,8,9,14,22,23 Known splice variants are classified as truncating.…”

“…8 SHaRe nontruncating MYBPC3 missense variants (Tables S1, S2) were classified as previously reported 14 in accordance with American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) joint guidelines, leveraging available clinical and experimental data. 3,8,9,14,22,23 Known splice variants are classified as truncating. Since variants in MYBPC3 present in gnomAD with allele frequencies of >4E-05 and absent in SHaRe are unlikely to be independently pathogenic for HCM, these variants were included in our list of benign MYBPC3 variants.…”

“…Since variants in MYBPC3 present in gnomAD with allele frequencies of >4E-05 and absent in SHaRe are unlikely to be independently pathogenic for HCM, these variants were included in our list of benign MYBPC3 variants. 14 More details regarding variant interpretation are provided within the Supplemental materials.…”

“…[10][11][12][13] Thus, interpretation of these truncating variants as pathogenic is straightforward. 14 However, the interpretation of missense variants within MYBPC3 presents a major challenge. Single amino acid substitutions (missense variants) are found commonly in healthy populations.…”

“…Thus, many missense variants lack sufficient evidence to be classified as either pathogenic or benign and are classified as variants of uncertain significance (VUS). 14,15 While identifying pathogenic variants allows for predictive genetic testing in at-risk relatives, 16 a VUS is not clinically actionable and may lead to misinterpretation by clinicians and patients. 17 Identification of a pathogenic sarcomere genetic variant for HCM also has important prognostic implications.…”