Lysosomal TMEM63A forms a voltage-gated and lipid-activated cation channel regulating TFEB signaling and maintaining CNS myelination

Lysosomal ion channels are emerging regulators of organelle homeostasis, yet how voltage- and lipid-dependent ion conductance is coupled to lysosomal transcriptional programs remains poorly understood. TMEM63A has been genetically linked to central nervous system (CNS) myelination, but its subcellular function and underlying mechanism are unclear. Here, using Tmem63a knockout mice, we found that loss of Tmem63a caused myelin abnormalities in the corpus callosum, increased seizure susceptibility, and exacerbated myelin damage in two in vivo models, supporting a physiological role of TMEM63A in CNS myelin integrity. Transcriptomic profiling further revealed abnormal expression of endolysosome-related genes in Tmem63a -deficient brains. Direct patch-clamp recordings of endolysosomal membranes showed that TMEM63A generates a voltage-gated nonselective cation (VGNC) current at the sub-nanoampere scale. Lysosomal TMEM63A-VGNC channels conduct both monovalent and divalent cations, including Ca 2+ , and their voltage sensitivity is regulated by charged residues within cytosolic and luminal regions of the transmembrane segments. Moreover, an endogenous lysophospholipid and a synthetic small molecule activated lysosomal TMEM63A channels, promoting lysosomal biogenesis and autophagy through transcription factor EB signaling. Our findings identify TMEM63A as a voltage-gated and lipid-activated lysosomal cation channel that links lysosome–TFEB signaling to CNS myelin homeostasis, revealing a critical role of lysosome ion channel in preserving myelin integrity.