Diagnostic testing for Rett syndrome by DHPLC and direct sequencing analysis of the MECP2 gene: identification of several novel mutations and polymorphisms

Am J Hum Genet. 2000 Dec;67(6):1428-36. doi: 10.1086/316913. Epub 2000 Oct 30.


Rett syndrome (RTT) is an X-linked dominant neurodevelopmental disorder affecting 1/10,000-15,000 girls. The disease-causing gene was identified as MECP2 on chromosome Xq28, and mutations have been found in approximately 80% of patients diagnosed with RTT. Numerous mutations have been identified in de novo and rare familial cases, and they occur primarily in the methyl-CpG-binding and transcriptional-repression domains of MeCP2. Our first diagnostic strategy used bidirectional sequencing of the entire MECP2 coding region. Subsequently, we implemented a two-tiered strategy that used denaturing high-performance liquid chromatography (DHPLC) for initial screening of nucleotide variants, followed by confirmatory sequencing analysis. If a definite mutation was not identified, then the entire MECP2 coding region was sequenced, to reduce the risk of false negatives. Collectively, we tested 228 unrelated female patients with a diagnosis of possible (209) or classic (19) RTT and found MECP2 mutations in 83 (40%) of 209 and 16 (84%) of 19 of the patients, respectively. Thirty-two different mutations were identified (8 missense, 9 nonsense, 1 splice site, and 14 frameshifts), of which 12 are novel and 9 recurrent in unrelated patients. Seven unclassified variants and eight polymorphisms were detected in 228 probands. Interestingly, we found that T203M, previously reported as a missense mutation in an autistic patient, is actually a benign polymorphism, according to parental analysis performed in a second case identified in this study. These findings highlight the complexities of missense variant interpretation and emphasize the importance of parental DNA analysis for establishing an etiologic relation between a possible mutation and disease. Overall, we found a 98.8% concordance rate between DHPLC and sequence analyses. One mutation initially missed by the DHPLC screening was identified by sequencing. Modified conditions subsequently enabled its detection, underscoring the need for multiple optimized conditions for DHPLC analysis. We conclude that this two-tiered approach provides a sensitive, robust, and efficient strategy for RTT molecular diagnosis.

MeSH terms

  • Alleles
  • Amino Acid Substitution / genetics
  • Base Sequence
  • Chromatography, High Pressure Liquid / methods
  • Chromosomal Proteins, Non-Histone*
  • DNA Mutational Analysis / methods
  • DNA-Binding Proteins / genetics*
  • False Negative Reactions
  • Female
  • Genetic Testing / methods*
  • Genetic Variation / genetics
  • Humans
  • Male
  • Methyl-CpG-Binding Protein 2
  • Molecular Sequence Data
  • Mutation / genetics*
  • Pedigree
  • Polymorphism, Genetic / genetics*
  • Prenatal Diagnosis / methods
  • Repressor Proteins*
  • Reproducibility of Results
  • Rett Syndrome / diagnosis*
  • Rett Syndrome / genetics*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA


  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • MECP2 protein, human
  • Methyl-CpG-Binding Protein 2
  • Repressor Proteins

Associated data

  • GENBANK/X99686