Congenital Variant Rett Syndrome: FOXG1 Gene Deletion/Duplication

Condition Description

Mutations and deletions of the FOXG1 gene (14q13) cause a developmental disorder known as a Congenital Variant of Rett syndrome.  Common features include severe postnatal microcephaly, severe intellectual disability with absent language, apraxia, hypogenesis of the corpus callosum, jerky movements and generalized seizures.  These individuals have normal body measurements at birth but then have slow growth after leading to low weight and low normal stature.  Sleep was reported to be disrupted starting in infancy and stereotypical hand movements were observed.  Unlike Rett syndrome, individuals with a FOXG1 mutation do NOT have any periods of normal development.  

Duplications of the FOXG1 gene have been associated with developmental epilepsy, intellectual disability, and severe speech impairment.  

For patients with suspected Congenital Variant of Rett syndrome, sequence analysis is recommended as the first step in mutation identification. For patients in whom mutations are not identified by full gene sequencing, deletion/duplication analysis is appropriate.

  • Kortum et al. (2011). J Med Genet, 48:396-406.
  • OMIM #613454: Congenital Variant Rett syndrome
  • OMIM #164874: FOXG1 gene

Genes (1)

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This test is indicated for:
  • Confirmation of a clinical diagnosis of Congenital Variant Rett syndrome in an individual in whom sequence analysis was negative.
  • Carrier testing in adults with a family history of Congenital Variant Rett syndrome in whom sequence analysis was negative.


DNA isolated from peripheral blood is hybridized to a CGH array to detect deletions and duplications. The targeted CGH array has overlapping probes which cover the entire genomic region.


Detection is limited to duplications and deletions. The CGH array will not detect point or intronic mutations. Results of molecular analysis must be interpreted in the context of the patient's clinical and/or biochemical phenotype.

Specimen Requirements

Listed below are EGL's preferred sample criteria. For any questions, please call 470.378.2200 and ask to speak with a laboratory genetic counselor (
Submit only 1 of the following specimen types
Whole Blood (EDTA)

EDTA (Purple Top)
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Collection and Shipping
Ship sample at room temperature for receipt at EGL within 72 hours of collection. Do not freeze.
DNA, Isolated

Isolation using the Perkin Elmer™Chemagen™ Chemagen™ Automated Extraction method or Qiagen™ Puregene kit for DNA extraction is recommended.
Collection and Shipping
Refrigerate until time of shipment in 100 ng/µL in TE buffer. Ship sample at room temperature with overnight delivery.

Special Instructions

Sequence analysis is required before deletion/duplication analysis by targeted CGH array. If sequencing is performed outside of EGL Genetics, please submit a copy of the sequencing report with the test requisition.
  • Sequence analysis of the FOXG1 gene is available and is required before deletion/duplication analysis.  
  • Custom diagnostic mutation analysis (KM) is available to family members if mutations are identified by targeted mutation testing or sequencing analysis.
  • Prenatal testing is available only for known familial mutations to individuals who are confirmed carriers of mutations. Please contact the laboratory genetic counselor to discuss appropriate testing prior to collecting a prenatal specimen.

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