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Lissencephaly-4 with Microcephaly via the NDE1 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
NDE1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11873NDE181479 81479,81479 $990 Order Options and Pricing

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

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

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

Lissencephalies and subcortical band heterotopia (SBH) are a group of cerebral malformations involving arrest of neuronal migration during embryogenesis. Lissencephaly is characterized by simplification or absence of the brain convolutions, resulting in a smooth appearance. SBH, also known as double cortex, is characterized by abnormal bands of neurons beneath a normal cortex. Lissencephalies and SBH are characterized by intellectual disability and seizures. Additional features include microcephaly, subtle dysmorphic features, failure to thrive, difficulty feeding and swallowing, malformations of the digits, muscle spasms, myoclonic jerks, cognitive impairment, and poor social interactions (Leventer et al. 2001. PubMed ID: 11502906; Wallerstein et al. 2008. PubMed ID: 18462864; Dobyns. 2010. PubMed ID: 20331703; Di Donato et al. 2017. PubMed ID: 28440899). The incidence of lissencephalies is ~1:100,000 live births (https://www.orpha.net).

Lissencephalies are clinically and genetically heterogeneous. Several forms are recognized. They are distinguished on the basis of the clinical features and the causative genes.

Lissencephaly-4 with microcephaly (LIS4) is characterized by extreme congenital microcephaly, and profound global developmental delay. Additional features include short stature, macrosomia, prominent broad nasal bridge, and hypertonia. MRI findings include grossly simplified cortical gyral structure, agenesis of the corpus callosum and a hypoplastic cerebellum (Alkuraya et al. 2011. PubMed ID: 21529751; Bakircioglu et al. 2011. PubMed ID: 21529752).


Lissencephaly-4 with microcephaly is inherited in an autosomal recessive manner. To date, 3 homozygous pathogenic variants (one splicing, one small frameshift deletion and one small frameshift duplication) in the NDE1 gene have been reported in five consanguineous families from the Middle East (Alkuraya et al. 2011. PubMed ID: 21529751; Bakircioglu et al. 2011. PubMed ID: 21529752).

The NDE1 gene encodes Nude Neurodevelopment protein 1, a member of the nuclear distribution E family. It is involved in several cellular functions, including the development of the cerebral cortex and neuronal migration (Feng and Walsh. 2004. PubMed ID: 15473967; Shu et al. 2004. PubMed ID: 15473966).

Clinical Sensitivity - Sequencing with CNV PGxome

Pathogenic variants in the NDE1 gene appear to be rare. To date, only three pathogenic variants have been implicated in five consanguineous families from the Middle East (Alkuraya et al. 2011. PubMed ID: 21529751; Bakircioglu et al. 2011. PubMed ID: 21529752). All reported pathogenic variants are detectable by sequencing.

Testing Strategy

This test provides full coverage of all coding exons of the NDE1 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Candidates for this test are patients with lissencephaly with or without microcephaly. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in NDE1.


Official Gene Symbol OMIM ID
NDE1 609449
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Lissencephaly 4 AR 614019
Microhydranencephaly AR 605013


  • Alkuraya et al. 2011. PubMed ID: 21529751
  • Bakircioglu et al. 2011. PubMed ID: 21529752
  • Di Donato et al. 2017. PubMed ID: 28440899
  • Dobyns. 2010. PubMed ID: 20331703
  • Feng and Walsh. 2004. PubMed ID: 15473967
  • Leventer et al. 2001. PubMed ID: 11502906
  • Shu et al. 2004. PubMed ID: 15473966
  • Wallerstein et al. 2008. PubMed ID: 18462864


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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

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2) Select Additional Test Options

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