A form of autosomal dominant juvenile myoclonic epilepsy is caused by a nonconservative missense mutation, A322D, in the GABA A receptor ␣1 subunit M3 transmembrane helix. We reported previously that the A322D mutation reduced total and surface ␣1(A322D) subunit protein and that residual ␣1(A322D) subunit resided in the endoplasmic reticulum. Here, we demonstrate that the reduction in ␣1(A322D) expression results from rapid endoplasmic reticulum-associated degradation of the ␣1(A322D) subunit through the ubiquitin-proteasome system. We provide direct evidence that the ␣1(A322D) subunit misfolds and show that in at least 33% of ␣1(A322D) subunits, M3 failed to insert into the lipid bilayer. We constructed a series of mutations in the M3 domain and empirically determined the apparent free energy cost (⌬G app) of membrane insertion failure, and we show that the ⌬G app correlated directly with the recently elucidated transmembrane sequence code (⌬G Lep). These data provide a biochemical mechanism for the pathogenesis of this epilepsy mutation and demonstrate that ⌬G Lep predicts the efficiency of lipid partitioning of a naturally occurring protein's transmembrane domain expressed in vivo. Finally, we calculated the ⌬⌬G Lep for 277 known transmembrane missense mutations associated with Charcot-Marie-Tooth disease, diabetes insipidus, retinitis pigmentosa, cystic fibrosis, and severe myoclonic epilepsy of infancy and showed that the majority of these mutations also are likely to destabilize transmembrane domain membrane insertion, but that only a minority of the mutations would be predicted to be as destabilizing as the A322D mutation.ion channel ͉ peripheral myelin protein ͉ protein folding ͉ sodium channel ͉ translocon G ABA A receptors, the major inhibitory neurotransmitter receptors in the mammalian central nervous system, are pentameric ligand-gated ion channels whose five subunits originate from seven families containing multiple subtypes but most commonly assemble with two ␣1 subunits, two 2 subunits, and one ␥2 subunit (1-3). In mammalian cells, expression of an ␣-subunit is required to form functional receptors (4). GABA A receptors are homologous to other types of ligand-gated ion channels in the cys-loop receptor ion channel superfamily, which also includes glycine, serotonin type three, and nicotinic acetylcholine receptors (AChR). Cryoelectron microscopy experiments elucidated the three-dimensional structure of the transmembrane domains of the Torpedo AChR to a resolution of 4Å (5), and it is assumed that the GABA A receptor structure is similar (6). Each GABA A receptor subunit contains four transmembrane helices (M1-M4). One M2 domain from each subunit lines the ion channel pore and is surrounded by M1, M3, and M4 helices.A nonconservative missense mutation (A322D) in the M3 domain of the GABA A receptor ␣1 subunit gene (GABRA1) causes autosomal dominant juvenile myoclonic epilepsy (ADJME) (7). Electrophysiological experiments demonstrated that the A322D mutation altered GABA A receptor function (7-9)....