Diagnostic Test Directory

Molecular Genetics Laboratory

CHOP in the News

Clinical Lab Products quotes Avni Santani, PhD, Scientific Director, Molecular Genetics Laboratory, in a story about next-gen sequencing. Read the story »

Laboratory Update

Testing for the Noonan spectrum of disorders is now available at the Molecular Genetics Laboratory. Learn more about Noonan spectrum testing »

Congenital Variant of Rett Syndrome (FOXG1 Deletion-Duplication Analysis)

  • LIS Mnemonic: MBFOXG1DEL


    Collect whole blood in a purple top (EDTA) tube (preferred). Extracted DNA is acceptable.

    Volume Required

    5ml whole blood or 1 ug extracted DNA

    Minimum Required

    3ml whole blood


    Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday within 24 hours of collection.


    Whole blood can be refrigerated until shipment.

    Unacceptable conditions

    Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens.

    Specimen Handling

    Do not heat, freeze or centrifuge blood before shipment. Refrigerate sample until shipment.

Days Performed

Mon - Fri 9:00am to 4:00pm


4-6 weeks



Disease Information

Clinical Features:

Classic Rett syndrome is a severe neurodevelopmental disorder that primarily affects females. While classic Rett syndrome is defined on the basis of strict diagnostic criteria, atypical forms of Rett do exist that vary in terms of age of onset (congenital and late regression variants) as well as symptom severity (preserved speech variant). In the congenital variant form, girls are floppy and retarded from the very first months of life. The majority of congenital variants do not bear MECP2 or CDKL5 mutations, with only four cases being reported with MECP2 mutations. Very recently, truncating mutations in the FOXG1 gene have been identified in these patients.

Molecular Genetics:

FOXG1 is located on 14q12. It encodes the forkhead box protein G1, FoxG1, a transcriptional factor with expression restricted to fetal and adult brain and testis. Truncating mutations have been identified in two patients with the congenital variant of Rett syndrome. Large deletions of the 14q12 region encompassing the FOXG1 gene as well as an inversion of the FOXG1 gene have also been described in some patients.

Test Methods:

Large deletions and duplications will be detected using multiplex ligation-dependent probe amplification assay (MLPA).

Detection Rate:

Mutations in the FOXG1 have been identified in the congenital variant form of RTT syndrome. Overall, sequence and deletiona analysis will identify mutations in about 4% of RTT patients that are MECP2 and CDKL5 negative. The analytical sensitivity of this assay is 99%.

Related Tests:

Sequence analysis of the FOXG1 gene is available. Known mutation analysis of the FOXG1 gene is available to family members for mutations previously identified by sequence analysis or deletion/duplication analysis. Prenatal testing is available to individuals who are confirmed carriers of mutations in the FOXG1 gene. Please contact the laboratory director to discuss appropriateness of testing prior to collecting a prenatal specimen.


Test results with interpretation will be mailed and/or faxed to the referring physician following completion of the test. Additional reports will be provided as requested.


The clinical utility of the assay is to support a clinical diagnosis of the disease, facilitate genetic counseling, assess the risk to other first degree relatives and to facilitate testing of at - risk family members.

Search Lab Test Directory

Search by disease or test name

View a full list of all lab tests

Contact Us

Ask for more information about our laboratory services.