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Juvenile Batten disease is a fatal neurodegenerative disorder caused by mutations in the CLN3 gene, whose function is unknown. CLN3 has a yeast orthologue, Btn1p, the function of which can be complemented by its human counterpart, indicating some conservation of CLN3 function between the two organisms. Wolfe et al. show that both the level and the subcellular location of yeast Btn1p is pH-dependent, suggesting that human CLN3 might share this complexity of regulation and shedding light on the pathology of Batten disease.