Transient Receptor Potential Canonical 6 (TRPC6) is a tetrameric Ca²⁺/Na⁺-permeable cation channel, and is expressed in various types of cells including podocytes in kidney glomerulus. Mutations of this gene are known to be associated with the two major causes of nephrotic syndrome (NS), namely minimal change nephrotic syndrome and focal segmental glomerular sclerosis. We have previously reported that a negative feedback regulation triggered by cellular Ca²⁺ elevation (calmodulin-mediated Ca²⁺-dependent inactivation, CDI) is impaired in NS-associated TRPC6 mutations. However, the pathophysiological significance of impaired CDI is largely unknown. In this study, we evaluated the activities of NS-associated TRPC6 channels by using the patch-clamp recording. The inactivation of inward currents in NS-associated mutations was significantly delayed compared to that of the wild-type, and their total current densities which were calculated by integrating the inward currents exhibited a strong correlation with the age at the disease presentation. To elucidate the functional importance of the channel surface expression or delayed inactivation, the CRISPR/Cas9 system was used to edit the TRPC6 gene in mouse podocyte MPC-5 cells. The established cell line expressing CDI impaired-TRPC6 exhibited excess currents, while the expression level of TRPC6 on the cell surface remained to be unchanged. These results indicated the impact of CDI on NS onset and progression, and suggested that evaluation of the CDI in TRPC6 may contribute to pathological prediction of the onset and prognosis of NS.