The APOL1 protective M1 modifier occurs exclusively with the KIK protein haplotype to suppress channel conductance

Introduction. Genetic studies have shown the APOL1 variant p.N264K, also called M1, is associated with markedly lower kidney disease risk when co-inherited with the G2-risk allele. Empirical studies show M1 in cis with G2 blocks APOL1 cation channel flux. To date M1 only occurs on a specific APOL1 haplotype defined by three amino acid positions: p.Lys150 (K), p.Ile228 (I) and p.Lys255 (K). We analyzed two large community datasets to determine if M1 occurs on other APOL1 protein haplotypes and used a cell model to assess if the M1 variant alone is sufficient to block channel activity or if its haplotype context modifies its function. Methods. Phased APOL1 haplotypes frequencies were examined in the Alzheimer Disease Sequencing Project Release 5 (ASDP R5) participants (n=40,909) and confirmed in All of Us Research Program (All of Us) enrollees (n=72,538). Reported race was compared with genetically inferred ancestry. Local APOL1 genealogies were inferred and allele age determined. Thallium flux was measured in 293 cells after induced expression of APOL1-G2 on natural and engineered haplotype backgrounds. Results. The M1 variant occurred exclusively on the KIK APOL1 protein haplotype in all ADSP R5 participants (n=330) and 99.5% of All of Us participants (n=3,560). Local genealogies placed these chromosomes within the lineage carrying p.150K. In vitro thallium flux assays demonstrated that M1 alone and p.Lys150 alone each partially reduced thallium flux but completely abrogated thallium flux when on the same haplotype. Conclusions. M1 is inherited almost exclusively with a single haplotype background. Both the p.150K and p.264K (M1) are needed to completely block APOL1-G2-mediated thallium flux. Studies aimed at examining and exploiting the protective mechanisms of M1 for possible treatments need to consider its distinct haplotype context.