Liver fat accumulation contributes to discordant genetic risk between coronary artery disease and type 2 diabetes

Background. Type 2 diabetes (T2D) and coronary artery disease (CAD) frequently co-occur, yet the biological pathways that jointly determine risk remain incompletely understood. Most genetic studies have examined shared risk from a single-disease perspective, limiting insight into the mechanisms that generate discordant risk between conditions. Methods. We applied PLACO to multi-ancestry GWAS data of T2D and CAD to identify shared loci, prioritising shared causal signals using colocalisation. Shared variants were clustered by their associations with 77 cardiometabolic traits, and cluster-specific genetic risk scores (GRS) were tested for association with 17 clinical biomarkers and 1,254 binary outcomes in 378,772 UK Biobank (UKB) participants. Two-sample Mendelian randomisation (MR) was used to test the causal role of liver fat. Results. We identified 149 loci shared between T2D and CAD; most novel loci had discordant effects (35 of 42), in contrast to the predominantly concordant signals reported previously. Clustering 187 independent shared variants revealed seven mechanistic clusters, three of them centred on liver fat and defined by discordant T2D?CAD effects. Enrichment analyses and cluster-GRS associations in UKB highlight associations between higher liver fat and T2D risk with a cardioprotective lipid profile and reduced CAD risk. Genetically higher liver fat increased T2D risk but lowered CAD risk in MR analyses; partitioning liver fat instruments by their effect on ApoB-containing lipoproteins indicates that the CAD effects are determined more by effects of circulating ApoB rather than liver fat itself. Conclusions. Liver fat largely sets the direction of T2D risk, whereas the fate of that lipid, retained in the liver with low circulating ApoB or exported as ApoB-containing lipoproteins, sets the direction of CAD risk. This liver-centric partitioning provides a mechanistic framework for the discordant cardiometabolic effects of hepatic lipid and lipid-lowering pathways, with implications for precision prevention.