Conclusions The membrane trafficking and mitochondrial deficits uncovered in homozygous CbCln3Δex7/8 cells are likely to particularly impact neuronal function. Neurotransmission heavily relies on membrane vesicle transport, and a high-energy metabolism may further sensitize neurons to the loss of battenin activity. Thus, our panel of wild-type, heterozygous, and homozygous CbCln3Δex7/8 cerebellar cells provide an ideal model system to further elucidate battenin function and JNCL pathogenesis.