Mutations in the Na+-HCO3- co-transporter (NBC1) cause permanent proximal renal tubular acidosis (pRTA) with ocular abnormalities. However, little has been known about the relationship between the degree of NBC1 inactivation and the severity of pRTA. This study identified three new homozygous mutations (T485S, A799V, and R881C) in the common coding regions of NBC1. Functional analysis of these new as well as the known mutants (R298S and R510H) in Xenopus oocytes revealed a considerable variation in their electrogenic activities. Whereas the activities of R298S, A799V, and R881C were 15 to 40% of the wild-type (WT) activity, T485S and R510H, as a result of poor surface expression, showed almost no activities. However, T485S, like R510H, had the transport activity corresponding to approximately 50% of the WT activity in ECV304 cells, indicating that surface expression of T485S and R510H varies between the different in vitro cell systems. Electrophysiologic analysis showed that WT, R298S, and R881C all function with 2HCO3- to 1Na+ stoichiometry and have similar extracellular Na+ affinity, indicating that reduction in Na+ affinity cannot explain the inactivation of R298S and R881C. These results, together with the presence of nonfunctional mutants (Q29X and DeltaA) in other patients, suggest that at least approximately 50% reduction of NBC1 activity would be required to cause severe pRTA.