Abstract

Background: Hypertrophic cardiomyopathy (HCM) is a genetically heterogeneous disorder primarily linked to rare variants in sarcomere genes, though recently certain non-sarcomeric genes have emerged as important contributors. Non-Mendelian genetic variants with reproducible moderate effect sizes and low penetrance—intermediate-effect variants (IEVs)—, can play a crucial role in modulating disease expression. Understanding the clinical impact of IEVs is crucial to unravel HCM's complex genetic architecture. Methods: We conducted an ancestry-based enrichment analysis of 14 validated HCM genes, including the nine-core sarcomere and five non-sarcomere genes (ALPK3, CSRP3, FHOD3, FLNC, TRIM63). Enrichment of intermediate frequency missense variants was evaluated in 10,981 HCM cases vs 4,030 internal-controls of European-ancestry, and in 590,000 external-controls from gnomAD non-Finnish Europeans. Population-Attributable Fraction (PAF) was calculated to assess IEVs' contribution to HCM. Age-related disease penetrance, phenotypic severity (LVMWT), and major adverse cardiac events (MACE) were analyzed in 11,991 HCM cases of the whole cohort according to five genetic groups: genotype-negative, isolated IEV, monogenic, monogenic + IEV, and double monogenic. Results: Fourteen IEVs in eight genes were identified in 731 individuals (6.1% of the cohort), of whom 570 patients (4.8%) had IEVs in isolation: 198 (34.7%) in sarcomeric genes and 372 (65.3%) in non-sarcomeric genes. Contribution of IEVs to HCM genetics according to PAF was estimated to be 4.9% (CI95%: 3.2%-6.7%). A significant gradient in penetrance, phenotypic severity, and MACE was observed across genetic groups. Compared to genotype-negative patients, IEV carriers displayed a younger median age at diagnosis (59 years; CI95%: 46–69 vs 61 years; CI95%: 49–70; p=0.0073) and a higher mean LVMWT (18.1±3.7 vs 19.0±4.3; p=0.0043). IEVs also modified disease expression in individuals with monogenic variants causing a more aggressive phenotype than individuals from the Monogenic-only group with HCM onset at younger age and a higher LVMWT (all p<0.0001), being MACE-free survival significantly lower (93.3% vs 69.3% at age 70; p<0.0001). Conclusions: IEVs are present in 6.1% of HCM cases and account for 4.8% of HCM genetic burden. IEVs also influence disease severity and outcomes, particularly when combined with monogenic disease-causing variants. Evaluation of IEVs should be considered when performing HCM genetic testing.