NGS for Diagnosis of Rett Syndrome and Related Disorders

March 2024
Ampath | ampath.co.za

Overview

Rett syndrome is a spectrum of neurological disorders predominantly affecting females, ranging from:

• Classic Rett syndrome
• Atypical (variant) Rett syndrome
• Milder learning disabilities

Classic Rett Syndrome:

• Most often caused by pathogenic variants in the MECP2 gene (X chromosome)
• Severe and progressive
• Onset after apparently normal development (6–18 months)
• Followed by:
  • Developmental plateau
  • Rapid skill regression
  • Stereotypic movements
  • Seizures
  • Acquired microcephaly
  • Ataxia
  • Dysautonomia

MECP2-Related Disorders in Males:

• Range from:
  • Severe neonatal encephalopathy
  • Pyramidal signs
  • Parkinsonism
  • Macroorchidism (PPM-X syndrome)
  • Severe intellectual disability

Genetic Heterogeneity

While MECP2 variants account for the majority of classic Rett cases:

• ~5% of classic Rett cases
• ~25% of atypical Rett cases
  ...do not show MECP2 mutations.

Variants in other genes can mimic Rett syndrome clinically:

Other Relevant Genes:

• CDKL5 – Early seizure onset, atypical Rett
• FOXG1 – Congenital Rett presentation
• MEF2C – Overlapping features with Rett
• UBE3A – Accounts for ~11% of Angelman syndrome cases; features overlap with Rett

Diagnostic Testing at Ampath

Historically:

• Targeted Sanger sequencing for MECP2 hotspots was used.

Now:

• Next Generation Sequencing (NGS) on the Ion Torrent platform offers comprehensive coverage
• Combined with MLPA (Multiplex Ligation-dependent Probe Amplification)
• Detects both point mutations and deletions/duplications
• Similar cost to older methods, but broader and more effective

Genes and Testing Methods Included

Ampath's NGS panel includes the following genes:

✅ MECP2

• Inheritance: X-linked dominant
• Presentation: Classic Rett syndrome
• Method: NGS (Exons 1–4) + MLPA (Exons 1–4)

✅ CDKL5

• Inheritance: X-linked dominant
• Presentation: Atypical Rett
• Method: NGS (Exons 2–18) + MLPA (Exons 3, 6, 9, 10)

✅ FOXG1

• Inheritance: Autosomal dominant
• Presentation: Atypical Rett
• Method: NGS (Exon 1)

✅ MEF2C

• Inheritance: Autosomal dominant
• Presentation: Atypical Rett
• Method: NGS (Exons 2–11)

✅ UBE3A

• Inheritance: Autosomal dominant
• Presentation: Angelman syndrome
• Method: NGS (Exons 3–13)

🔎 Note: UBE3A accounts for ~11% of Angelman syndrome.
First-line testing for Angelman syndrome should be requested separately using a methylation-sensitive MLPA technique.

Test Information

• Mnemonic: RETT
• Genes covered: MECP2, CDKL5, FOXG1, MEF2C, UBE3A
• Specimen: Peripheral blood sample (EDTA)
• Turnaround time: 6 weeks (from receipt at the National Reference Laboratory)
• Cash price (2024): R5,224.00

📞 For more information:
Tel: 012 678 0645
Email: geneticsclinic@ampath.co.za