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. TRANSLATIONAL STATEMENT: G1 and G2 coding variants in APOL1 increase the risk of kidney disease in populations with African ancestry. Another coding variant p.N264K (M1) reduces kidney disease risk when inherited in cis with the APOL1 G2 risk allele. Here we show in large populations that the M1 is almost always inherited on an APOL1 haplotype that encodes a p.E150K amino acid change. Otherwise G2 in the absence of M1 is exclusively on a p.150E haplotype. M1 and p.150K functionally interact to block APOL1-mediated thallium flux in cell culture models. These functional interactions highlight the importance of considering the M1 variant in its haplotype context when designing basic research studies and translating results into future approaches for therapeutic intervention.