FLCN phosphorylation was first identified by Baba et al. (2006), when multiple FLCN bands were seen on Western blots. Additionally, FLCN was identified in a screen of phosphorylated peptides (Gauci et al., 2009). Further research has shown that serine 62 (ser62) is a phosphorylation site in FLCN and that it is indirectly up-regulated by AMPK (Wang et al., 2010). FLCN also appears to be phosphorylated at ser302 by unknown kinases downstream of mTORC1 (Piao et al., 2009). Since mTORC1 is known to be indirectly down-regulated by AMPK, this process could be associated with a feedback mechanism that regulates mTOR signalling. Indeed, mTORC1 was subsequently found to phosphorylate ser62 and ser73 of FLCN (Yu et al., 2011).

Phosphorylation of these residues appears to be cell-cycle dependent: ser62 and ser73 become phosphorylated as the cell cycle progresses, with maximum phosphorylation seen during the mitotic phase (Dephoure et al., 2008; Laviolette et al., 2013). FLCN with phosphorylated ser62 and ser73 residues shows reduced stability, suggesting this modification is important for cell cycle regulation (Laviolette et al., 2013). Additionally, S302 is highly phosphorylated during G₁ phase (Dephoure et al., 2008).

ULK1 inhibits FLCN’s interaction with GABARAP by phosphorylating three novel phosphorylation sites in the C-terminus of FLCN at S406, S537 and S542 (Dunlop et al., 2014). Mapping these residues on to the crystal structure of FLCN’s C-terminal DENN domain shows that they are all on the solvent-exposed surface of the protein, and are thus accessible for phosphorylation (Dunlop et al., 2014). ULK1 was still able to dissociate the interaction of GABARAP and a triple serine-to-alanine FLCN mutant in vivo, suggesting that other phosphorylation sites in FLCN, GABARAP or the FNIP proteins also control this interaction (Dunlop et al., 2014). Two further ULK1 phosphorylation sites were identified at FLCN S316 and T317, but these are poorly conserved between species (Dunlop et al., 2014).

FLCN has also been found to be ubiquitinated on lysine 206 and 559 (Wagner et al., 2011). Danielsen et al. (2011) also noted FLCN ubiquitinylation, but did not delineate specific residues. The relevance of these post-translational FLCN modifications is yet to be determined, however.