Polygenic architecture of rare coding variation across 400,000 exomes

Abstract

Both common and rare genetic variants influence complex traits and common diseases. Genome-wide association studies have discovered thousands of common-variant associations, and more recently, large-scale exome sequencing studies have identified rare-variant associations in hundreds of genes1-3. However, rare-variant genetic architecture is not well characterized, and the relationship between common- and rare-variant architecture is unclear4. Here, we quantify the heritability explained by gene-wise burden of rare coding variants and compare the genetic architecture of common and rare variation across 22 common traits and diseases in 400,000 UK Biobank exomes5. Rare coding variants (AF = 1e-6 - 1e-3) explain 1.3% (SE = 0.03%) of phenotypic variance on average - much less than common variants - and most burden heritability is explained by ultra-rare loss-of-function variants (AF = 1e-6 - 1e-5). Common and rare variants implicate the same cell types, with similar enrichments, and they have pleiotropic effects on the same pairs of traits, with similar genetic correlations. They partially colocalize at individual genes and loci, but not to the same extent: burden heritability is strongly concentrated in a limited number of significant genes (median: 6 genes explaining 19% of h2), while common-variant heritability is much more polygenic. Burden heritability is also more strongly concentrated in constrained genes (median enrichment: 4.5x vs. 2.1x for common variants), indicating that negative selection affects common- and rare-variant architecture differently. Finally, we find that burden heritability for schizophrenia and bipolar disorder6,7 is approximately 2%. Our results show that there are a tractable number of large-effect genes to discover by studying rare variants, that common and rare associations are mechanistically convergent, and that rare coding variants will contribute only modestly to missing heritability and population risk stratification.