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X-Linked Lissencephaly-2 via the ARX 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
ARX 81404 81404,81403 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
10003ARX81404 81404,81403 $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

Lissencephalies are a group of cerebral malformations due to an arrest of neuronal migration during embryogenesis. They are characterized by simplification or absence of the brain convolutions, resulting in a smooth appearance. Lissencephalies 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, and poor social interactions (Leventer et al. 2001. PubMed ID: 11502906; Wallerstein et al. 2008. PubMed ID: 18462864).

Lissencephalies are clinically and genetically heterogeneous. Several forms are recognized. They are distinguished by the clinical features and causative genes. Lissencephaly X-linded 2 can be distinguished by ambiguous genitalia, hypothalamic dysfunction, hypotonia, hyperreflexia, intractable epilepsy, agenesis of the corpus callosum, and thickened cortex (Bonneau et al. 2002. PubMed ID: 11891829; Kato et al. 2004. PubMed ID: 1472291; Dobyns et al. 1999. PubMed ID: 10494089; Marsh et al. 2009. PubMed ID: 19439424). Onset is neonatal in males, and death occurs early. Female carriers may be unaffected or mildly affected (Marsh et al. 2009. PubMed ID: 19439424).


Lissencephaly X-linked 2 is caused by pathogenic variants in the ARX gene (Kitamura et al. 2002. PubMed ID: 12379852; Bonneau et al. 2002. PubMed ID: 11891829; Kato et al. 2004. PubMed ID: 14722918). To date, ~ 30 pathogenic variants have been implicated in the disease. Two thirds of the variants are truncating and include nonsense, splice site, small frameshift deletions or insertions, and large deletions. The remaining variants are missense (Human Gene Mutation Database).

ARX encodes the Aristaless-related homeobox transcription factor, which plays a crucial role in cerebral development and patterning (Bienvenu et al. 2002. PubMed ID: 11971879).

Clinical Sensitivity - Sequencing with CNV PG-Select

Pathogenic variants in the ARX gene have been detected in about 4% of patients from a large cohort of children with lissencephaly (Di Donato et al. 2018. PubMed ID: 29671837).

Testing Strategy

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

Indications for Test

Candidates for this test are patients with X-linked lissencephaly with ambiguous genitalia.


Official Gene Symbol OMIM ID
ARX 300382
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Bienvenu et al. 2002. PubMed ID: 11971879
  • Bonneau et al. 2002. PubMed ID: 11891829
  • Di Donato et al. 2018. PubMed ID: 29671837
  • Dobyns et al. 1999. PubMed ID: 10494089
  • Human Gene Mutation Database (Bio-base).
  • Kato et al. 2004. PubMed ID: 14722918
  • Kitamura et al. 2002. PubMed ID: 12379852
  • Leventer et al. 2001. PubMed ID: 11502906
  • Marsh et al. 2009. PubMed ID: 19439424
  • 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

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View Ordering Instructions

1) Select Test Method (Platform)

1) Select Test Type

2) Select Additional Test Options

No Additional Test Options are available for this test.

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