Multi-functional protein, involved in both the cellular response to amino acid availability and in the regulation of glycolysis (By similarity). GTPase-activating protein that plays a key role in the cellular response to amino acid availability through regulation of the mTORC1 signaling cascade controlling the MiT/TFE factors tfeb and tfe3. Regulates glycolysis by binding to lactate dehydrogenase ldha, acting as an uncompetitive inhibitor (By similarity). Activates mTORC1 by acting as a GTPase-activating protein: specifically stimulates GTP hydrolysis by rragc/RagC or rragd/RagD, promoting the conversion to the GDP-bound state of rragc/RagC or rragd/RagD, and thereby activating the kinase activity of mTORC1. The GTPase-activating activity is inhibited during starvation and activated in presence of nutrients. In low-amino acid conditions, the lysosomal folliculin complex (LFC) is formed on the membrane of lysosomes, which inhibits the GTPase-activating activity of flcn, inactivates mTORC1 and maximizes nuclear translocation of tfeb and tfe3. Upon amino acid restimulation, rraga/RagA (or rragb/RagB) nucleotide exchange promotes disassembly of the LFC complex and liberates the GTPase-activating activity of flcn, leading to activation of mTORC1 and subsequent cytoplasmic retention of tfeb and tfe3. Required for the exit of hematopoietic stem cell from pluripotency by promoting mTOR-dependent cytoplasmic retention of tfe3, thereby increasing Wnt signaling (By similarity). Acts as an inhibitor of browning of adipose tissue by regulating mTOR-dependent cytoplasmic retention of tfe3 (By similarity). In response to flow stress, regulates STK11/LKB1 accumulation and mTORC1 activation through primary cilia. Required for starvation-induced perinuclear clustering of lysosomes by promoting association of rilp with its effector rab34 (By similarity). Involved in the control of embryonic stem cells differentiation; together with lamtor1 it is necessary to recruit and activate rragc/RagC and rragd/RagD at the lysosomes, and to induce exit of embryonic stem cells from pluripotency via non-canonical, mTOR-independent tfe3 inactivation (By similarity). GTPase-activating activity is inhibited in the folliculin complex (LFC), which stabilizes the GDP-bound state of rraga/RagA (or rragb/RagB), because Arg-164 is located far from the rragc/RagC or rragd/RagD nucleotide pocket. Disassembly of the LFC complex upon amino acid restimulation liberates the GTPase-activating activity. Component of the lysosomal folliculin complex (LFC). Localizes to lysosome membrane in amino acid-depleted conditions and relocalizes to the cytosol upon refeeding. Also localizes to motile and non-motile cilia, centrosomes and the mitotic spindle. Belongs to the folliculin family.