The APOL1 variant p.N264K blocks 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-G2s 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 non-toxic 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 non-toxic APOL1 M1-G2 span the membrane four times, forming a potential ion channel. Interestingly, molecular dynamics analyses further revealed that in M1-G2, 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 non-toxic 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.