Gephyrin (GPHN) is an organizational protein that clusters and localizes the inhibitory glycine (GlyR) and GABA A receptors to the microtubular matrix of the neuronal postsynaptic membrane. Mice deficient in gephyrin develop a hereditary molybdenum cofactor deficiency and a neurological phenotype that mimics startle disease (hyperekplexia). This neuromotor disorder is associated with mutations in the GlyR ␣ 1 and  subunit genes (GLRA1 and GLRB). Further genetic heterogeneity is suspected, and we hypothesized that patients lacking mutations in GLRA1 and GLRB might have mutations in the gephyrin gene (GPHN). In addition, we adopted a yeast two-hybrid screen, using the GlyR  subunit intracellular loop as bait, in an attempt to identify further GlyR-interacting proteins implicated in hyperekplexia. Gephyrin cDNAs were isolated, and subsequent RT-PCR analysis from human tissues demonstrated the presence of five alternatively spliced GPHN exons concentrated in the central linker region of the gene. This region generated 11 distinct GPHN transcript isoforms, with 10 being specific to neuronal tissue. Mutation analysis of GPHN exons in hyperekplexia patients revealed a missense mutation (A28T) in one patient causing an amino acid substitution (N10Y). Functional testing demonstrated that GPHN N10Y does not disrupt GlyR-gephyrin interactions or collybistininduced cell-surface clustering. We provide evidence that GlyR-gephyrin binding is dependent on the presence of an intact C-terminal MoeA homology domain. Therefore, the N10Y mutation and alternative splicing of GPHN transcripts do not affect interactions with GlyRs but may affect other interactions with the cytoskeleton or gephyrin accessory proteins.Neuronal postsynaptic membranes contain a wide variety of ion channels and receptor proteins that contribute to the balance of excitatory and inhibitory neurotransmission in the human central nervous system. Mature postnatal neuroinhibition is mediated by postsynaptic glycinergic and GABA A 1 receptor systems that are structurally related to the nicotinic receptors with a typical pentameric structure constructed from heterogeneous subunit constituents containing four transmembrane (TM) domains and a large intracellular loop between TM3 and TM4 (1, 2). These subunits combine to form fast response, ligand-gated chloride channels that modify excitatory neurotransmission in the human brainstem and spinal cord (3-5). Inhibitory glycine receptors (GlyRs) are composed of three ligand-binding ␣ 1 subunits (GlyR ␣ 1 ) and two structural  subunits (GlyR ) that are anchored and clustered on the postsynaptic membrane of inhibitory neurons by the interaction of a motif within the TM3-TM4 loop of the GlyR subunit with anchoring protein, gephyrin (6 -8). In contrast to GlyRs, there is a lack of evidence for a direct physical interaction between gephyrin and GABA A receptor subunit(s) (7, 9), although immunohistochemical studies have detected co-localization of gephyrin with major subtypes of GABA A receptors at GABAergic postsynaptic...