Coding, modifier, and regulatory effects shape circulating APOL1 levels

APOL1 variants G1 and G2 are major genetic risk factors for chronic kidney disease in people with recent sub-Saharan African ancestry, yet the mechanisms linking genotype to disease remain poorly defined. Circulating APOL1 is likely to play a critical role, although how specific genotypes and regulatory variants influence circulating APOL1 levels is incompletely understood. We analysed Olink-measured APOL1 NPX (Normalized Protein eXpression) levels from 43 587 UK Biobank participants. Associations between APOL1 NPX and known genotypes were assessed in individuals with recent sub-Saharan African ancestry, including analyses of G1, G2, E150K (rs2239785) and N264K (rs73885316). We also investigated protein quantitative trait loci and cis-acting variants across the APOL1 locus, including predicted microRNA binding sites. Results indicated that APOL1 NPX varied in an APOL1 genotype-dependent manner. E150K, G1, and G2 demonstrate a clear dose-dependent relationship with APOL1 NPX, with the largest effect for G2. After accounting for APOL1 genotype, APOL1 NPX remained higher in individuals with self-reported Black or Black British ethnicity, consistent with additional regulatory elements. Multiple cis-regulatory variants near APOL1 were independently associated with APOL1 NPX, and are likely to contribute to ancestry-related differences. Together these findings demonstrate that APOL1 genotype is a major determinant of APOL1 NPX, and that G1 and G2 have distinct biological effects. Regulatory variation adds another layer of control over APOL1 NPX and may help explain population differences. These findings provide a biological framework for understanding genotype-specific molecular effects of APOL1 variation.