Candidate gene analysis in Rett syndrome and the identification of 21 SNPs in Xq.

Rett syndrome (RTT) is an X-linked dominant neurodevelopmental disorder that affects females. Exclusion mapping studies using a new family with maternal inheritance of RTT defined Xq28 as the candidate region for the RTT gene. Six candidate genes were selected for mutation analysis based on their established expression patterns and known functions in the CNS. These are: Glutamate receptor subunit 3 (GLUR3), GABA receptor subunit alpha 3 (GABRA3), GABA receptor subunit e1 (GABRE1), Vacuolar ATPase subunit 1 (VATPS1, XAP3), the human homologue of plexin 3-SEX (XAP6) and the Synaptobrevin-like protein (SYBL1). Major rearrangements involving these genes were excluded by Southern analysis. No disease-causing mutations were found, but several single-nucleotide polymorphisms (SNPs) were detected. These SNPs will be useful in future linkage analysis and whole-genome association studies for other diseases. The genomic characterization of GLUR3 and GABRA3 will allow mutational analysis of these genes as candidates for other X-linked neurological disorders mapping to Xq25-Xq26 and Xq28.