Catalyzes the trimethylation of 'Lys-116' in calmodulin. [calmodulin]-L-lysine + S-adenosyl-L-methionine = [calmodulin]-N(6)-methyl-L-lysine + H(+) + S-adenosyl-L-homocysteine Monomer (By similarity). Interacts with HSP90, probably as a client. Isoform 1 is expressed in brain, liver, muscle colon and lung. Isoform 2 is expressed in colon, testis, kidney and brain. Isoform 1 and isoform 2 are expressed in normal lymphoblastoid cells but not in lymphoblastoid cells from patients with hypotonia-cystinuria syndrome. The gene represented in this entry is involved in disease pathogenesis. A homozygous 77.4-kb deletion that disrupts the gene represented in this entry, PREPL, and SLC3A1, causes atypical hypotonia-cystinuria syndrome, characterized by mild to moderate intellectual disability and respiratory chain complex IV deficiency. Belongs to the class I-like SAM-binding methyltransferase superfamily. CLNMT methyltransferase family.