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Compton-North Congenital Myopathy via the CNTN1 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
CNTN1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11183CNTN181479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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


  • Angela Gruber, PhD

Clinical Features and Genetics

Clinical Features

Compton-North congenital myopathy (OMIM 612540) is a severe, congenital myopathy with fetal akinesia and distinct secondary losses of beta-2-syntrophin and alpha-dystrobrevin observed in muscle biopsy.  Among a large cohort of patients with myopathies of unknown etiology, Jones et al. (Neuromusc Disord 13:456-467, 2003) found a small subset of patients with deficiencies of one or more components of the syntrophin–dystrobrevin subcomplex, a part of the dystrophin-glycoprotein complex which anchors the extracellular matrix to the intracellular cytoskeleton of muscle cells.  An affected sibship in this group of patients was further studied by Compton et al. (Am J Hum Genet 83:714-724, 2008).  Clinical findings in the affected sibship included reduced fetal movement, polyhydramnios, premature birth, severe hypotonia, absent deep tendon reflexes, and skeletal, bulbar, and respiratory weakness (Compton et al. 2008; Jones et al. 2003).  One patient survived to one month of age with intubation while the remaining three died shortly after birth.  Dysmorphic features were also reported.  These included scaphocephaly, an oval-shaped face, hypertelorism, and a high-arched palate. Findings of the hands and fingers included simian creases, arachnodactyly, overlapping fingers, and camptodactyly.  Serum CpK levels were normal.  Skeletal muscle biopsy showed myopathic changes including minor variation in fiber size, and there was no indication of dystrophic changes.  Immunohistochemical and western blot analysis revealed decreased or absent beta-2-syntrophin and alpha-dystrobrevin at the muscle sarcolemma (Compton et al. 2008).  Genetic analysis ruled-out mutations in the genes encoding these proteins (Jones et al. 2003) and, instead, homozygous mutations in the contactin-1 (CNTN1) gene were found (Compton et al. 2008).


Compton-North congenital myopathy is inherited as an autosomal recessive disorder.  Thus far only one family has been diagnosed with CNTN1 mutations.  Affected members of the reported family were found to be homozygous for a frame-shift mutation (Compton et al. 2008). Contactin-1, a neural immunoglobulin family adhesion protein, is expressed at the neuromuscular junction as well as in the central and peripheral nervous system.  It has been proposed that loss of contactin-1 at the neuromuscular junction impairs communication or adhesion between nerve and muscle leading to defective neuromuscular transmission, similar to that seen in congenital myasthenic syndrome (Compton et al. 2008).

Clinical Sensitivity - Sequencing with CNV PGxome

Thus far Compton-North congenital myopathy has been diagnosed molecularly in a single sibship from consanguineous parents of Egyptian origin (Compton et al. 2008). Clinical and analytical sensitivity cannot be estimated due to the paucity of reported cases.

Testing Strategy

This test provides full coverage of all coding exons of the CNTN1 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

Severe, congenital myopathy preceded by fetal akinesia. Muscle biopsies with deficiency of beta 2-syntrophin and alpha-dystrobrevin. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CNTN1.


Official Gene Symbol OMIM ID
CNTN1 600016
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Myopathy, Congenital, Compton-North AR 612540


  • Compton AG, Albrecht DE, Seto JT, Cooper ST, Ilkovski B, Jones KJ, Challis D, Mowat D, Ranscht B, Bahlo M, Froehner SC, North KN. 2008. Mutations in Contactin-1, a Neural Adhesion and Neuromuscular Junction Protein, Cause a Familial Form of Lethal Congenital Myopathy. The American Journal of Human Genetics 83: 714724. PubMed ID: 19026398
  • Jones K., Compton A., Yang N, Mills M., Peters M., Mowat D, Kunkel L., Froehner S., North K. 2003. Deficiency of the syntrophins and ?-dystrobrevin in patients with inherited myopathy. Neuromuscular Disorders 13: 456467. PubMed ID: 12899872


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

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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