The a subunit is the largest of 15 different subunits that make up the vacuolar H(+)-ATPase (V-ATPase) complex, where it functions in proton translocation. In mammals, this subunit has four paralogous isoforms, a1–a4, which may encode signals for targeting assembled V-ATPases to specific intracellular locations. Despite the functional importance of the a subunit, its structure remains controversial. By studying molecular mechanisms of human disease–causing missense mutations within a subunit isoforms, we may identify domains critical for V-ATPase targeting, activity and/or regulation. cDNA-encoded FLAG-tagged human wildtype ATP6V0A2 (a2) and ATP6V0A4 (a4) subunits and their mutants, a2(P405L) (causing cutis laxa), and a4(R449H) and a4(G820R) (causing renal tubular acidosis, dRTA), were transiently expressed in HEK 293 cells. N-Glycosylation was assessed using endoglycosidases, revealing that a2(P405L), a4(R449H), and a4(G820R) were fully N-glycosylated. Cycloheximide (CHX) chase assays revealed that a2(P405L) and a4(R449H) were unstable relative to wildtype. a4(R449H) was degraded predominantly in the proteasomal pathway, whereas a2(P405L) was degraded in both proteasomal and lysosomal pathways. Immunofluorescence studies disclosed retention in the endoplasmic reticulum and defective cell-surface expression of a4(R449H) and defective Golgi trafficking of a2(P405L). Co-immunoprecipitation studies revealed an increase in association of a4(R449H) with the V(0) assembly factor VMA21, and a reduced association with the V(1) sector subunit, ATP6V1B1 (B1). For a4(G820R), where stability, degradation, and trafficking were relatively unaffected, 3D molecular modeling suggested that the mutation causes dRTA by blocking the proton pathway. This study provides critical information that may assist rational drug design to manage dRTA and cutis laxa.