Introduction: Atrial fibrillation (AF) is the most common sustained arrhythmia and is associated with substantial morbidity and mortality. AF is known to have a heritable component, with >100 associated common variant loci. Rare variant studies have yielded limited robust associations for AF. We aimed to utilize large genome and exome sequencing data to discover rare genetic variants conferring large effects on AF risk.

Methods: We meta-analyzed genome and exome sequencing data from 36 studies, including TOPMed, CCDG, UK Biobank and FOURIER. We performed exome-wide gene burden testing of rare (MAF<0.1%) loss-of-function and deleterious missense variants, and single variant testing of low-frequency and rare (MAF<1%) coding variants. Within genome sequenced samples, we performed gene burden testing of rare structural variants. Novel signals were replicated in MyCode. Finally, we functionally validated a novel gene by siRNA knockdown in pluripotent-induced atrial cardiomyocytes.

Results: We included 52,416 AF cases and 277,762 controls, of which 49.6% were female, 83.4% were of European ancestry, and the mean baseline age was 56 years. In analysis of rare coding variation, we identified 4 novel genes associated with AF, including MYBPC3 (OR 3.5, P=2.1x10^-15), LMNA (OR 5.7, P=8.8x10^-11), PKP2 (OR 1.9, P=5.2x10^-8) and KDM5B (OR 2.3, P=3.0x10^-6). These signals were robust to removal of heart failure and cardiomyopathy cases and were replicated in independent datasets. Single variant analysis identified 2 novel signals in FAM189A2 (OR 3.9, P=7.86x10^-8) and ZFC3H1 (OR 5.9, P=9.7x10^-8). Rare deletions in CTNNA3 (OR 4.5, P=7.0x10^-9) were associated with increased AF risk and were supported by independent coding variant analyses, while duplications of GATA4 (OR 0.24, P=2.1x10^-5) were associated with reduced AF risk. In functional studies, knockdown of KDM5B resulted in shortening of the atrial action potential duration.

Conclusions: Our analyses show the contribution of rare coding and structural variants to AF risk, highlight the shared genetic pathways underlying cardiomyopathy and AF, and implicate the histone demethylase gene KDM5B in AF susceptibility. In sum, we expanded our understanding of the rare variant architecture of this common arrhythmia.