Background and objectiveSequence variants in genes involved in absorption of cholesterol and other sterols may promote understanding of the impact of dietary components, as opposed to endogenous synthesis, on circulating cholesterol levels and the risk of coronary artery disease (CAD).We aim to examine the effect of rare coding variants of the ABCG5 and ABCG8 genes, encoding key proteins regulating sterol absorption (ATP-binding cassette G5 and G8), on levels of non-HDL-C and phytosterols, and corresponding risk of CAD.Methods and resultsWe examined all coding sequence variants of ABCG5 and ABCG8, identified through whole-genome sequencing of 8,453 Icelanders and subsequently imputed into a large population-based dataset, for association with non-HDL-C (n= 136,672). Identified variants were then tested for association with CAD (39,904 cases/306,338 controls) and phytosterol levels (n=2,721).We found three rare missense variants of ABCG5 (p.Tyr250His and p.Gly27Ala) and ABCG8 (p.Gln271Arg) that associate with levels of non-HDL-C (p.Tyr250Hisβ=0.42 SD, P=5.9x10, p.Gly27Alaβ=0.26, P=1.3x10, and p.Gln271Argβ=0.25, P=2.7x10) phytosterols, and two of them also with CAD risk (p.Tyr250HisOR=1.97, P=4.9x10, p.Gly27AlaOR=2.08, P=5.1x10, and p.Gln271ArgOR=1.35, P=0.11). Further, we identified two sisters, homozygous for a rare missense variant p.Arg263Gln of ABCG8 with extremely high levels of phytosterols and early onset CAD, compatible with sitosterolemia, an autosomal recessive disorder. No homozygous carrier for the ABCG8 protein truncating mutation p.Trp361Ter, the most commonly reported cause of sitosterolemia, was identified in Iceland, but heterozygosity for this rare mutation had insignificant effects on cholesterol and phytosterol levels, and CAD.ConclusionOur data demonstrate that rare coding variants of ABCG5 and ABCG8, affect circulating cholesterol and phytosterols and the risk of CAD. The results raise the possibility that subtle defects in the encoded proteins or in their regulation may underlie the variable responses to diets in the general population.