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Autosomal-Recessive Intellectual Disability via the NRXN1 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
NRXN1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4849NRXN181479 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


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Autosomal-recessive intellectual disability (AR-ID) or Pitt-Hopkins-like syndrome 2 (PTHLS2; OMIM:614235) is a clinically and genetically heterogeneous disorder. Recessive mutations in the gene NRXN1 result in AR-ID with the following features: severe intellectual disability, tonic-clonic seizures with infantile onset, motor delay, reduced or absent speech, stereotypic motions, constipation, abnormal sleep-wake cycle and strabismus (Zweier et al. Am J Hu Genet 85(5):655-666, 2009; Harrison et al. Am J Med Genet A 155A(11):2826-2831, 2011; Duong et al. Am J Med Genet B 159B(3) :354-358,2012).


AR-ID is inherited in an autosomal recessive manner and can be caused by mutations in the NRXN1 gene. Both point mutations and gross deletions of NRXN1 have been reported in cases of AR-ID. Heterozygous variants in NRXN1 have been associated with Autism Spectrum Disorder (ASD) as well as other neurological disorders, however no direct causative link has been demonstrated (Gregor et al. BMC Med Genet 12:106, 2011). NRXN1 encodes a protein in the neurexin family. Neurexins are transmembrane proteins that localize to presynaptic termini. Neurexins possess an extracellular domain that interacts with neuroligin proteins that are found on post-synaptic membranes. Neurexin-neuroligin binding is important for formation and stabilization of synapses (Craig and Kang. Curr Opin Nuerobiol 17(1):43-52, 2007). In addition to their role in synaptogenesis, neurexins are also required for efficient neurotransmitter release at synapses (Dudanova et al. J Neurosci 26(41):10599-10613, 2006). Genes encoding other neurexin and neuroligin interacting proteins, such as SHANK3 and CASK, have also been implicated in ID disorders, suggesting a shared etiology (Zweier et al., 2009).

Clinical Sensitivity - Sequencing with CNV PG-Select

NRXN1 mutations were found in <1% of patients diagnosed with the ID disorder Pitt-Hopkins syndrome who lacked the common TCF4 mutation (Zweier et al. Am J Hu Genet 85(5):655-666, 2009).

Approximately 60% of reported recessive NRXN1 variants are gross deletions (Zweier et al. Am J Hu Genet. 85(5):655-666, 2009; Harrison et al. Am J Med Genet A 155A(11):2826-2831, 2011; Duong et al. Am J Med Genet B 159B(3):354-358, 2012).

Testing Strategy

This test provides full coverage of all coding exons of the NRXN1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for NRXN1 sequencing and copy number assessment include patients with symptoms of AR-ID with a family history consistent with autosomal recessive inheritance. Individuals diagnosed with Pitt-Hopkins syndrome, but for which no TCF4 mutation was identified, are also candidates for NRXN1 sequencing (Zweier et al., 2009). This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in NRXN1.


Official Gene Symbol OMIM ID
NRXN1 600565
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Pitt-Hopkins-like syndrome 2 AR 614325


  • Craig, A.M. and Kang, Y. (2007). "Neurexin-neuroligin signaling in synapse development." Curr Opin Neurobiol 17(1):43-52. PubMed ID: 17275284
  • Dudanova, I. et al. (2006). "Important contribution of alpha-Neurexins to Ca2+-triggered exocytosis of secretory granules." J Neurosci 26(41):10599-10613. PubMed ID: 17035546
  • Duong, L. et al. (2012). "Mutations in NRXN1 in a family muliply affected with brain disorders: NRXN1 mutations and brain disorders." Am J Med Genet B 159B(3):354-358. PubMed ID: 22337556
  • Gregor, A. et al. (2011). "Expanding the clinical spectrum associated with defects in CNTNAP2 and NRXN1." BMC Med Genet 12:106. PubMed ID: 21827697
  • Harrison, V. et al. (2011). "Compound Heterozygous Deletion of NRXN1 Causing Severe Developmental Delay With Early Onset Epilepsy in Two Sisters." Am J Med Genet A 155A(11):2826-2831. PubMed ID: 21964664
  • Zweier, C. et al. (2009). "CNTNAP2 and NRXN1 Are Mutated in Autosomal-Recessive Pitt-Hopkins-like Mental Retardation and Determine the Level of a Common Synaptic Protein in Drosophila." Am J Hu Genet 85(5):655-666. PubMed ID: 19896112


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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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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