Plays an important role in amino acid transport by acting as binding partner of amino acid transporters SLC6A18 and SLC6A19, regulating their trafficking on the cell surface and their activity (By similarity). May also play a role in trafficking of amino acid transporters SLC3A1 and SLC7A9 to the renal cortical cell membrane (By similarity). Regulator of SNARE complex function (By similarity). Stimulator of beta cell replication (By similarity). Monomer. Homodimer; dimerization prevents CLTRN cleavage by BACE2 (By similarity). Interacts with SLC6A18; this interaction regulates the trafficking of SLC6A18 to the cell membrane and its amino acid transporter activity. Interacts with SLC6A19; this interaction regulates the trafficking of SLC6A19 to the cell membrane and its amino acid transporter activity (By similarity). Interacts with SNAPIN (By similarity). Localizes to the brush border membranes of cells in the proximal tubules of kidney. Colocalized with SLC6A19 in the early proximal S1 tubule. The cleavage site containing the double Phe-Phe motif acts as negative regulator of shedding by BACE2. Glycosylated. Glycosylation is required for plasma membrane localization and for its cleavage by BACE2. Proteolytically processed in pancreatic beta cells by BACE2 leading to the generation and extracellular release of soluble CLTRN, and a corresponding cell-associated C-terminal fragment which is later cleaved by gamma-secretase. This shedding process inactivates CLTRN (By similarity). Three cleavage sites have been identified for BACE2, two clustered sites after Phe-116 and Leu-118 and a more membrane proximal site at Phe-125; the preferred BACE2 cleavage site seems to be between Phe-125 and Leu-126, Phe-116 and Leu-118 act as alternative sites (By similarity). Belongs to the CLTRN family.