The APOL1 variant p.N264K is predicted to block ion flow by occluding a pore at the cell surface

The APOL1 gene variants G1 and G2 are associated with an increased risk of APOL1-mediated kidney disease. A recently identified variant, p.N264K (M1), mitigates this risk of renal damage by abolishing APOL1-G2’s associated cytotoxicity. However, the molecular and structural basis of this protective effect remains incompletely understood. In this study, we first show that both the cytotoxic G2 and the nontoxic M1-G2 exhibit similar intracellular localization, surface expression, and turnover kinetics. Moreover, N-glycosylation assays indicated no differences in topology, and 3D models demonstrated that both cytotoxic G2 and nontoxic APOL1 M1-G2 span the membrane four times, forming a potential ion channel. Interestingly, molecular dynamics analyses of a computational APOL1 3D model further revealed that in case of M1, the lysine at position 264 occludes this channel, thereby preventing ion pore activity of APOL1. These findings provide, for the first time, a mechanistic explanation for the nontoxic behavior of the APOL1 M1-G2 variant. Additional 3D analyses suggest that the C-terminal region may contribute to APOL1 multimerization, potentially influencing ion flux and cytotoxicity.