Nearly all cases of Rett syndrome are caused by a mutation in the methyl CpG binding protein 2 (MECP2) (pronounced as meck-pea-two) gene. Scientists identified this gene-which is believed to control the functions of many other genes-in 1999. The MECP2 gene contains instructions for the synthesis of a protein called methyl cytosine binding protein 2 (MeCP2), which is needed for brain development and acts as one of the many biochemical switches that can either increase gene expression or tell other genes when to turn off and stop producing their own unique proteins. Because the MECP2 gene does not function properly in individuals with Rett syndrome, insufficient amounts or structurally abnormal forms of the protein are produced and can cause other genes to be abnormally expressed.
Not everyone who has an MECP2 mutation has Rett syndrome. Scientists have identified mutations in the CDKL5 and FOXG1 genes in individuals who have atypical or congenital Rett syndrome, but they are still learning how these mutations work. Scientists believe that the remaining cases may be caused by partial gene deletions, mutations in other parts of the gene, or additional genes that have not yet been identified, and they continue to look for other causes.
This answer is based on source information from National Institute of Neurological Disorders and Stroke.