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The MECP2 (meck-pea-two) gene contains instructions for the synthesis of a protein called "methyl cytosine binding protein 2" (MeCP2), which acts as one of the many biochemical switches that tell other genes when to turn off and stop producing their own unique proteins.

When the MECP2 gene does not function properly, as in those having Rett syndrome, insufficient amounts or structurally abnormal forms of the protein are formed. The absence or malfunction of the protein likely causes other genes to be abnormally expressed.