The hereditary spastic paraplegia type 21 (SPG21) protein is a RAB7A effector that promotes non-canonical mTORC1-catalyzed TFEB phosphorylation and cytoplasmic retention

Hereditary spastic paraplegia type 21 (SPG21) is an inherited neurological disorder caused by mutations in the SPG21 gene, which encodes a protein named SPG21 or maspardin. Herein, we report that SPG21 localizes to endolysosomes through interaction with the GTP-bound form of RAB7A. Disease-associated SPG21 variants reduce expression of SPG21 and disrupt its endolysosomal localization in both non-neuronal cells and neurons. Consistent with this localization, functional dependency analysis links SPG21 to endolysosomal and mTORC1 signaling pathways. Biochemical studies reveal that SPG21 depletion does not affect phosphorylation of canonical mTORC1 substrates such as ULK1, S6K1, 4E-BP1, but reduces phosphorylation of the non-canonical mTORC1 substrate TFEB. This enhances nuclear localization of TFEB and upregulation of TFEB-target genes. We conclude that SPG21 acts as a RAB7A effector that promotes non-canonical mTORC1-catalyzed phosphorylation of TFEB, thereby suppressing its nuclear localization and transcriptional activity. These findings link SPG21 dysfunction to altered endolysosomal signaling, offering new insights into SPG21 pathogenesis.