We trace the cause of congenital myasthenic syndromes in two patients to mutations in the epsilon subunit of the muscle acetylcholine receptor (AChR). Both patients harbour deletion of an asparagine residue in the epsilon subunit (epsilonN436del) at the C-terminus of the cytoplasmic loop linking the third (M3) and fourth (M4) transmembrane domains. The presence of a null mutation in the second allele of the epsilon subunit shows that epsilonN346del determines the phenotype. Endplate studies show markedly reduced expression of the epsilonN346del-AChR and compensatory accumulation of fetal gamma-AChR. Expression studies in HEK cells reveal decreased expression of epsilonN436del-AChR and abnormally brief channel openings. Thus, neuromuscular transmission is compromised by AChR deficiency, fast channel kinetics of the epsilonN346del-AChR and incomplete phenotypic rescue by gamma-AChR. Single-channel kinetic analysis shows that the epsilonN436del shortens channel openings by reducing stability of the diliganded receptor: rates of channel closing and of ACh dissociation are increased and the rate of channel opening is decreased. In addition to shortening the M3-M4 loop, epsilonN436del shifts a negatively charged aspartic acid residue adjacent to M4; the effects of epsilonN436del are shown to result from shortening of the M3-M4 loop and not from juxtaposition of a negative charge to M4. To determine whether the consequences of epsilonN346del are subunit-specific, we deleted residues that align with epsilonN436 in beta, delta and alpha subunits. Each deletion mutant reduces AChR expression, but whereas the beta and delta mutants curtail channel open duration, the alpha mutant strikingly prolongs open duration. Kinetic analysis reveals that the alpha mutant increases the stability of the diliganded receptor: rates of channel closing and of ACh dissociation are decreased and the rate of channel opening is increased. The overall studies reveal subunit asymmetry in the contributions of the M3-M4 loops in optimizing AChR activation through allosteric links to the channel and the agonist binding site.