Variant Rett syndrome in a girl with a pericentric X-chromosome inversion leading to epigenetic changes and overexpression of the MECP2 gene

•We investigated the genetic basis of disease in a female patient with a RTT-like clinical presentation.•Geneomic studies, quantification of lymphocyte mRNA expression and methylation status of the promoter region of MECP2 gene were performed.•Karyotype analysis revealed a pericentric inversion in the X chromosome 46,X,inv(X)(p22.1q28).•The patient displayed hypomethylation and an overexpression of the MECP2 gene at the mRNA level in the lymphocytes.•We propose that the de-regulation of MECP2 expression in this patient may be due to alterations in long-range genomic interactions.