Glycine receptors (GlyR) belong to the pentameric ligand gated ion channel (pLGIC) superfamily and mediate fast inhibitory transmission in the vertebrate CNS. Disruption of glycinergic transmission by inherited mutations produces startle disease in man. Many startle mutations are in GlyRs and provide useful clues to the function of the channel domains. E103K is one of few startle mutations found in the extracellular agonist binding site of the channel, in loop A of the principal side of the subunit interface. Homology modelling shows that the side chain of E103 is close to that of R131, in loop E of the complementary side of the binding site, and may form a salt bridge at the back of the binding site, constraining its size. We investigated this hypothesis in recombinant human α1 GlyR by site directed mutagenesis and functional measurements of agonist efficacy and potency by whole-cell patch clamp and single channel recording. Despite its position near the binding site, E103K causes hyperekplexia by impairing the efficacy of glycine, its ability to gate the channel once bound, which is very high in wild type GlyR. Mutating E103 and R131 caused various degrees of loss-of-function in the action of glycine, whereas mutations in R131 enhanced the efficacy of the slightly bigger partial agonist sarcosine (N-methyl glycine). The effects of the single charge-swapping mutations of these two residues were largely rescued in the double mutant, supporting the possibility that they interact via a salt bridge which normally constrains the efficacy of larger agonist molecules.