The CHRNE gene encodes the epsilon subunit of the acetycholine receptor protein. Acetylcholine receptor is a ligand gated ion channel made up of alpha, beta, gamma, delta and epsilon subunits. The receptor changes subunit composition shortly after birth when the epsilon subunit replaces the gamma subunit seen in embryonic receptors. Mutations in the CHRNE gene result in congenital myasthenic syndrome, a disease characterized by muscle weakness.

Mutations in CHRNE can affect acetylcholine receptor functioning in three ways. It can produce a prolonged opening of the acetylcholine receptor channel resulting in slowed decay of end plate currents, calcium overload of the synaptic region and ultimately myopathy of the endplate and postsynaptic membrane. This is classified as congenital myasthenic syndrome 4A, slow channel (CMS4A). In congenital myasthenic syndrome 4B, fast channel (CMS4B), mutations result in brief opening of the channel, producing a rapid decay in endplate current, failure to achieve threshold depolarisation and subsequently, failure to fire an action potential. Mutations can also cause deficiency of acetylcholine at the endplate resulting in low amplitude of the miniature endplate potential and current. This is classified as congenital myasthenic syndrome 4C, associated with acetylcholine receptor deficiency (CMS4C).