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Choline acetyltransferase catalyzes the synthesis of acetylcholine at cholinergic nerves. Mutations in humanCHATcause a congenital myasthenic syndrome due to impaired synthesis of ACh; this severe variant of the disease is frequently associated with unexpected episodes of potentially fatal apnea. The severity of this condition varies remarkably, and the molecular factors determining this variability are poorly understood. Furthermore, genotype–phenotype correlations have been difficult to establish in patients with biallelic mutations. We analyzed the protein expression of phosphorylated ChAT of sevenCHATmutations, p.Val136Met, p.Arg207His, p.Arg186Trp, p.Val194Leu, p.Pro211Ala, p.Arg566Cys, and p.Ser694Cys, in HEK-293 cells to phosphorylated ChAT, determined their enzyme kinetics and thermal stability, and examined their structural changes. Three mutations, p.Arg207His, p.Arg186Trp, and p.Arg566Cys, are novel, and p.Val136Met and p.Arg207His are homozygous in three families and associated with severe disease. The characterization of mutants showed a decrease in the overall catalytic efficiency of ChAT; in particular, those located near the active-site tunnel produced the most seriously disruptive phenotypic effects. On the other hand, p.Val136Met, which is located far from both active and substrate-binding sites, produced the most drastic reduction of ChAT expression. Overall, CHAT mutations producing low enzyme expression and severe kinetic effects are associated with the most severe phenotypes.We investigated the expression and enzyme kinetics of seven phosphorylated choline acetyltransferase (ChAT) mutants causing congenital myasthenic syndrome. The enzyme kinetics of ChAT mutants expressed in HEK cells was investigated using the Fonnum method and the structure was analyzed using the Swiss-PdbViewer program. We found that ChAT mutants resulting in low protein expression and/or severe kinetic changes were those associated with the most severe phenotypes.