The mutation responsible for the juvenile form of Batten disease was mapped to a single gene, Cln3 (T. J. Lerner et al. (1995) Cell 82:949-957). Yeast Saccharomyces cerevisiae has an open reading frame, BTN1 (YHC3), that encodes the putative homologue of Cln3p. Primary structure comparison indicates that the human Cln3p and yeast Btn1p are 59% similar and 39% identical and they have similar hydropathy profiles. Gene disruption of BTN1 in yeast has no apparent effect on growth or viability of the cells under a variety of conditions. Gene fusion protein constructs of green fluorescent protein (GFP) and Btn1p, with GFP at the amino and carboxyl ends of Btn1p, localize to the vacuole in yeast. These data indicate that BTN1 is a nonessential gene under most growth conditions which functions in the vacuole in yeast Saccharomyces cerevisiae.