The presence of four nucleotide changes and a three base-pair deletion in the GABA A alpha6-subunit promoter is described in Sardinian alcohol non-preferring rats, selectively bred for their ethanol aversion. These mutations are associated with the R100Q alpha6 intragenic mutation that was previously characterized in the same animals. The possibility that these mutated nucleotides alter the ethanol-induced upregulation of the alpha6 gene was investigated by measuring cerebellar alpha6 mRNA levels after a chronic ethanol liquid diet in sNP rat. Real-time quantitative PCR showed an increased alpha6 gene expression after ethanol ingestion in normal and mutated rats. However, lower amounts of alpha6 mRNA levels were detected both in control and in ethanol-treated sNP rats carrying the five promoter and the intragenic mutations in a homozygous state. Using the electromobility shift assay, specific DNA binding sites were found in cerebellar extracts of the alpha6 regions comprising the five mutations. These results suggest that one or more of the mutated binding sites that were found in the 5' flanking alpha6 region may be a consensus sequence for regulatory factors which are responsible for both basal and ethanol-induced alpha6 gene expression.