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Revista chilena de pediatría

versión impresa ISSN 0370-4106

Rev. chil. pediatr. vol.90 no.2 Santiago abr. 2019 


Rett Syndrome: MECP2 gene molecular analysis in Chilean patients

Carolina Aron W.1 

Geraldinne Rauch L.1 

Felipe Benavides G.2 

M. Gabriela Repetto L.3 

1 Medical Student, Chile.

2 Biochemist, Chile.

3 Clinical geneticist, Facultad de Medicina, Centro de genética y genómica, Clínica alemana-Universidad del Desarrollo. Santiago, Chile.



Rett syndrome (RTT) is a progressive neurological disorder characterized by regres sion of psychomotor development in previously healthy girls. Most cases are due to pathogenic va riants in the MECP2 gene which encodes for the methyl CpG-binding protein 2.


To des cribe the frequency and type of pathogenic variants in the MECP2 gene in Chilean female patients with clinical diagnosis of RTT.

Patients and Method:

Chilean women with clinical suspicion of RTT were invited to participate in the study. Clinical data were collected through a questionnaire. MECP2 pathogenic variants were analyzed by Sanger sequencing method and Multiplex Ligation-dependent Probe Amplification (MLPA) was used to detect duplications or deletions.


The study in cluded 14 patients with suspected RTT, of which eight (57%) patients had pathogenic variants. The other patients remain without molecular diagnosis.


Pathogenic variants in MECP2 are present in Chilean patients with RTT. It is likely that there are other genes or diagnoses involved in patients without MECP2 findings. As of this study, molecular diagnosis is available in Chile.

Keywords: Rett Syndrome; MECP2; Methyl-CpG-Binding Protein 2


Rett syndrome (RTT; MIM#312750) is a neurode velopmental disorder that mainly affects girls and is considered virtually lethal in boys1. The incidence is estimated at 1 in 10,000 to 15,000 female live births2.

RTT is diagnosed based on clinical criteria3 and there are three clinical forms: classic or typical, variant or atypical, and mild learning disabilities, The latter is less frequent. Classical RTT is the most frequent pre sentation (75%)4. It is characterized by apparently nor mal development until 6 to 18 months of age, followed by a halt and subsequent regression in psychomotor development, with loss of manual skills, gait, language, and emergence of stereotypies. Atypical RTT has five possible variants: congenital, late regression, preserved speech, early epilepsy, and incomplete form, in which other genes may be involved1,2,3,4,5.

Although the diagnosis is clinical, molecular study allows confirmation Pathogenic variants in MECP2 gene are the cause of 80-90% of cases of classical RTT and about 40% of atypical RTT. Most of the variants are located in exons 3 and 4, and 99% of cases, they are de novo events1,2,3,4,5,6. The remaining cases have been asso ciated with pathogenic variants in CDKL5 and FOXG1 genes, which are more frequently found in the atypical Rett Syndrome form7,8.

MECP2 is located in Xq28 chromosome region, it is composed of four exons which encode the Methyl-CpG-binding protein2 , 9 ). This protein is involved in neuronal development and maturation, as well as in the differentiation and formation of neuronal synap ses, by regulating gene expression through CpG island methylation, acting both as a repressor and trans criptional activator10,11,12. The protein has four functio nal domains, of which the most important are MBD (Methyl-CpG-binding Domain) and TRD (Transcrip tional Repression Domain)1 , 11 ).

In Chile, the molecular bases of Rett syndrome has not been characterized. In this study, the type and fre quency of variants in MECP2 in Chilean patients with a clinical diagnosis of RTT were analyzed.

Patients and Method

Girls, members of the Fundación Síndrome de Rett Chile, with suspicion or clinical diagnosis of RTT, were invited to participate prior informed consent of their parents. The study was approved by the Research Ethics Committee of the Centro de Bioética de la Facul tad de Medicina Clínica Alemana Universidad del Desa rrollo, according to the Declaration of Helsinki13.

Clinical information was obtained through open- and closed-ended questionnaires, which included in formation about family history, perinatal history, and diagnostic criteria for Rett syndrome.

To detect variants and implement molecular diagnosis in the MECP2 gene, the gene was sequen ced through specific primers, designed using the Primer3 software for the coding region exons 1, 2, 3, and 414. The primers were verified using SNPCheck and BLAST15,16, and universal M13 tails were added to each primer to simplify the capillary sequencing procedure17. The exons were amplified by means of a touchdown program with extension at 68°-58°C for 1 minute, using MangoTaq polymerase (Bioline, UK). The Amplified PCR products were sequenced bidirec tionally with BigDye Terminator v1.1 following the manufacturer’s protocol (Thermo Fischer, USA). Mul tiplex ligation-dependent probe amplification (MLPA) kit P245 (MRC, Holland)18 was used to detect deletions or duplications in MECP2.


Fifteen women between the ages of 2 and 28 years, members of the Fundación Síndrome de Rett Chile par ticipated in the study. One patient was excluded becau se she did not meet the diagnostic criteria.

Out of the 14 patients, ten had classic RTT and four had atypical RTT characteristics. The collected infor mation did not allow to classify these patients into the subtypes of atypical RTT. (Table 1) describes the clinical manifestations.

Table 1 Clinical and molecular characteristics of the patients. 

Using Sanger sequencing, six pathogenic variants were found, five of them in patients with classic RTT presentation and one in a patient considered as aty pical RTT. Five of these pathogenic variants were in exons 3 and 4, and one in exon 2. In the eight patients in whom no variant was identified, deletion and du plication analysis were performed using MLPA. With this technique, one deletion of exon 3, pathogenic va riant, was detected in two additional patients: one with classical RTT and the other one with atypical form. In addition, one variant of uncertain significance (VUS) was found.

No pathogenic variants were found in the remai ning five patients (Table 2).

Table 2 Pathogenic variants identified in MECP2 gene. 


This is the first molecular study reported in Chile with RTT patients. Pathogenic variants were found in MECP2 in 57% of the studied patients.

In this group of participants, the frequency of clas sical RTT found was approximately 70% (10 patients), similar to that described in the literature (~75%)4, of which 60% (6 patients) had pathogenic variants of MECP2 and 10% (1 patient) a variant of uncertain significance (VUS). In the case of patients considered atypical RTT, 50% presented pathogenic variants in MECP2, which is similar to that reported in the litera ture6. The number of cases analysed was low, this is due to the low prevalence of this syndrome in the general population. In addition, the subtypes of patients with atypical RTT were not directly characterized, however, two of them have preserved speech and early psycho motor developmental delay, therefore, they may have some of these clinical variants.

Out of the eight pathogenic variants found, inclu ding deletions, four are among the most frequently des cribed variants (Arg106Trp, Thr158Met, Arg270Ter, and Arg306Cys)1,19. Although pathogenic variants in MECP2 occur de novo, there are more frequent va riants, probably due to the presence of mutational hotspots in this gene20. Deletions that include one or more exons have been observed in both patients with classic and atypical RTT21. This evidence suggests that it is important to use MLPA in cases where no specific variants have been found in the MECP2 gene. 87% of the found pathogenic variants are located in the MBD and TRD, in exons 3 and 4, as described in previous studies22,23.

An in-frame deletion of 36 nucleotides was found, c.1157_1192del36, classified as VUS. In this case, the analysis of the parents in the molecular diagnosis is im portant to classify this type of variants, but it has not yet been carried out in this family24.

This study is the first to report and document patho genic variants in MECP2 in patients with RTT in Chile. Knowing the specific pathogenic variants confirms the diagnosis and could allow the development of future molecular therapies. In girls, where there were no fin dings in MECP2, especially the two atypical patients, it would be interesting to evaluate the other genes related to the diagnosis of RTT, CDKL5, and FOXG1, as well as to consider differential RTT diagnoses.

After this work, the molecular examination for the MECP2 gene is available in Chile and, therefore, diag nostic certainty.

Ethical Responsibilities

Human Beings and animals protection: Disclosure the authors state that the procedures were followed ac cording to the Declaration of Helsinki and the World Medical Association regarding human experimenta tion developed for the medical community.

Data confidentiality: The authors state that they have followed the protocols of their Center and Local regu lations on the publication of patient data.

Rights to privacy and informed consent: The authors have obtained the informed consent of the patients and/or subjects referred to in the article. This docu ment is in the possession of the correspondence author.

Financial Disclosure: Authors state that no economic support has been asso ciated with the present study.

Conflicts of Interest: Authors declare no conflict of interest regarding the present study.

Aknowledgments: We thank “Fundación Síndrome de Rett Chile” and the families of the patients who motivated and parti cipated in this study. We also thank Mrs. Maria Luisa Guzman, RN and Ms. Valeria Tampe for technical as sistance.


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Received: May 04, 2018; Accepted: November 05, 2018

Correspondence: gabriela Repetto. E-mail:

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