We have isolated and sequenced a novel human gene (GABRE) of the GABAA neurotransmitter receptor family. A cDNA sequence of the gene coding for a 506 amino acid protein was identified, representing a member of a putative new class (epsilon) of the GABAA receptor. The gene is transcribed at least at low level in several different tissues, with the highest levels being detected in adult heart and placenta. Alternative splicing of GABRE transcripts isolated from different tissues was observed at multiple positions of the gene, yielding an unusually complex variety of cDNA variants. The structure of the 5' region of most cDNAs is compatible with expression of protein sequence epsilon only in adult brain, whereas in other tissues, the majority of transcripts code for truncated protein sequences. The GABRE gene extends over 14 kb and is clustered together with the alpha 3 and the putative beta 4 GABAA receptor subunit genes in an approximately 0.8-Mb interval in chromosome band Xq28, located in the candidate regions of two different neurologic diseases. Based on features of conservation of protein sequences, gene structure, and genomic organization of GABAA receptor gene clusters, we propose that the epsilon and gamma subunit genes have a common ancestor and that GABAA receptor gene clusters in the human genome have diverged by multiple duplication events of an ancestral gene cluster containing one each alpha, beta, and gamma/epsilon precursor gene.