Effect heterogeneity reveals complex pleiotropic effects of rare coding variants

Recent expansion of large-scale biobank resources has enabled rare-variant association studies (RVASs) and systematic investigation of rare-variant pleiotropy across thousands of phenotypes simultaneously. However, existing statistical frameworks for dissecting pleiotropy were largely developed for common-variant association signals and are not well suited to gene-based rare-variant burden signals, limiting the interpretation of cross-phenotype associations. Here, we develop Allelic Spectrum of Pleiotropy Informed Correlated Effects (ALLSPICE), a likelihood-based method that tests whether rare coding variant effects in genes exhibiting cross-phenotype associations are proportional or heterogeneous across continuous traits while accounting for phenotypic correlation using summary statistics. ALLSPICE is well calibrated in simulations and is implemented as an R package for scalable analysis of gene-level rare-variant burden associations. We applied ALLSPICE to RVAS of 359 continuous traits in the UK Biobank and identified 124 significant heterogeneous events among 11,810 pairs of gene-trait associations. By identifying effect heterogeneity within genes associated with multiple phenotypes, ALLSPICE extends analysis of allelic heterogeneity to biobank-scale RVASs, clarifies shared and heterogeneous rare-variant architectures underlying cross-phenotype burden associations, and provides insight into rare-variant pleiotropy.