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Early Infantile Epileptic Encephalopathy via the SZT2 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
SZT2 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4259SZT281479 81479,81479 $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


  • Eric Bend, PhD

Clinical Features and Genetics

Clinical Features

Early infantile epileptic encephalopathy-18 (EIEE-18) is an early onset seizure disorder associated with intractable epilepsy and intellectual disability. Onset of tonic, tonic-clonic, or absence seizures occurs between 2 months and 4 years of age; these seizures are refractory to treatment with antiepileptic drugs (Basel-Vanagaite et al. 2013). EIEE18 patients have severe intellectual disability with limited ability to speak. EIEE18 patients are hypotonic as infants and have delayed developmental milestones, with inability to stand or walk. EEG recording of EIEE18 patients show non-specific epileptiform abnormalities. Characteristic MRI findings in EIEE18 patients include a thick corpus callosum and cavum septum pellucidum that persists beyond the infantile period (Basel-Vanagaite et al. 2013).


EIEE18 is inherited in an autosomal recessive manner and is cause by mutations in the SZT2 gene. Nonsense and splice site mutations have been reported in severe cases of EIEE18 and a single amino acid deletion was reported in a family with mild EIEE18-like features (Basel-Vanagaite et al. 2013; Falcone et al. 2013). SZT2 encodes a conserved protein of unknown function that is highly expressed in the brain and spinal cord (Frankel et al. 2009). SZT2 was first identified by a forward genetic screen for mice with a reduced seizure threshold; known epilepsy gene KCNQ2 was also identified by this screen (Frankel et al. 2009).

Clinical Sensitivity - Sequencing with CNV PG-Select

The frequency of SZT2 variants in epilepsy patients is currently unknown. All reported SZT2 variants are detectable via sequencing (Basel-Vanagaite et al. 2013; Falcone et al. 2013).

Testing Strategy

This test provides full coverage of all coding exons of the SZT2 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

SZT2 testing should be considered for patients with infantile onset intractable epilepsy and intellectual disability that have MRI evidence of thickened corpus callosum and/or persistent cavum septum pellucidum. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SZT2.


Official Gene Symbol OMIM ID
SZT2 615463
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Epileptic encephalopathy, early infantile, 18 AR 615476


  • Basel-Vanagaite L, Hershkovitz T, Heyman E, Raspall-Chaure M, Kakar N, Smirin-Yosef P, Vila-Pueyo M, Kornreich L, Thiele H, Bode H, Lagovsky I, Dahary D, et al. 2013. Biallelic SZT2 Mutations Cause Infantile Encephalopathy with Epilepsy and Dysmorphic Corpus Callosum. The American Journal of Human Genetics 93: 524–529. PubMed ID: 23932106
  • Falcone M, Yariz KO, Ross DB, Foster J, Menendez I, Tekin M. 2013. An Amino Acid Deletion inSZT2 in a Family with Non-Syndromic Intellectual Disability. PLoS ONE 8: e82810. PubMed ID: 24324832
  • Frankel WN, Yang Y, Mahaffey CL, Beyer BJ, O’Brien TP. 2009. Szt2 , a novel gene for seizure threshold in mice. Genes, Brain and Behavior 8: 568–576. PubMed ID: 19624305


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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