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Early Infantile Epileptic Encephalopathy and Rett-like Syndrome via the CDKL5 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
CDKL5 81406 81406,81405 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4121CDKL581406 81406,81405 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Early infantile epileptic encephalopathy 2 (EIEE2; OMIM:300672) is characterized by seizure onset between one week and five months of age, infantile hypotonia, severe developmental delay, intellectual disability with absent speech, stereotyped hand movements and deceleration of head growth (Bahi-Buisson and Bienvenu 2011). CDKL5-related EIEE may also be diagnosed as early-onset seizure variant of Rett syndrome (RTT) or Angelman syndrome (OMIM: 105830).


EIEE2 is inherited in an X-linked dominant manner. Most cases of EIEE2 are sporadic and are caused by de novo mutations in the CDKL5 gene. Many missense, nonsense, frameshift and splicing mutations in CDKL5 have been reported in EIEE2 or RTT-like cases. Large deletions encompassing one or more exons of CDKL5 have also been reported. Females are most commonly affected, but CDKL5 mutations have also been reported in males with epileptic encephalopathy (Liang et al. 2011). CDKL5 encodes a neuronally expressed protein kinase. CDKL5 has been shown to bind the transcriptional repressor MECP2 and phosphorylate it in vitro, suggesting a shared etiology for CDKL5 and MECP2-related disorders (Mari et al. 2005).

Clinical Sensitivity - Sequencing with CNV PG-Select

De novo CDKL5 mutations were reported in 7% (26 of 258) of female patients presenting with encephalopathy and infantile seizures (Bahi-Buisson et al. 2012).

Testing Strategy

This test provides full coverage of all coding exons of the CDKL5 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for CDKL5 testing include males or females with early infantile epileptic encephalopathy (Liang et al. 2011). CDKL5 testing should also be considered in females diagnosed with RTT who present with intractable seizures within the first weeks of life (Artuso et al. 2010).


Official Gene Symbol OMIM ID
CDKL5 300203
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Epileptic Encephalopathy, Early Infantile, 2 XL 300672


  • Artuso R, Mencarelli MA, Polli R, Sartori S, Ariani F, Pollazzon M, Marozza A, Cilio MR, Specchio N, Vigevano F, Vecchi M, Boniver C, et al. 2010. Early-onset seizure variant of Rett syndrome: Definition of the clinical diagnostic criteria. Brain and Development 32: 1724. PubMed ID: 19362436
  • Bahi-Buisson N, Bienvenu T. 2011. CDKL5-Related Disorders: From Clinical Description to Molecular Genetics. Molecular Syndromology. PubMed ID: 22670135
  • Bahi-Buisson N, Villeneuve N, Caietta E, Jacquette A, Maurey H, Matthijs G, Esch H Van, Delahaye A, Moncla A, Milh M, Zufferey F, Diebold B, et al. 2012. Recurrent mutations in the CDKL5 gene: Genotype-phenotype relationships. American Journal of Medical Genetics Part A 158A: 16121619. PubMed ID: 22678952
  • Liang J-S, Shimojima K, Takayama R, Natsume J, Shichiji M, Hirasawa K, Imai K, Okanishi T, Mizuno S, Okumura A, Sugawara M, Ito T, et al. 2011. CDKL5 alterations lead to early epileptic encephalopathy in both genders: CDKL5 Alterations in Both Genders. Epilepsia 52: 18351842. PubMed ID: 21770923
  • Mari F, Azimonti S, Bertani I, Bolognese F, Colombo E, Caselli R, Scala E, Longo I, Grosso S, Pescucci C, Ariani F, Hayek G, Balestri P, Bergo A, Badaracco G, Zappella M, Broccoli V, Renieri A, Kilstrup-Nielsen C, Landsberger N.. 2005. CDKL5 belongs to the same molecular pathway of MeCP2 and it is responsible for the early-onset seizure variant of Rett syndrome. Human Molecular Genetics 14: 19351946. PubMed ID: 15917271


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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