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Carnitine Palmitoyltransferase 1A Deficiency via the CPT1A 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
9297 CPT1A 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9297CPT1A81479 81479,81479 $890 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 backbone).

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

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

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • McKenna Kyriss, PhD

Clinical Features and Genetics

Clinical Features

Carnitine palmitoyltransferase 1A (CPT1A) deficiency is a disorder of long-chain fatty acid oxidation. Age of onset varies, but is typically in infancy or early childhood. Symptoms typically occur concurrently with febrile and/or gastrointestinal illness, and onset can be quite rapid. Patients present with hepatic encephalopathy which may lead to coma, hypoketotic hypoglycemia, liver failure indicated by elevated transaminases, fatty liver infiltration, transient hepatomegaly, elevated plasma carnitine and free fatty acids. In addition, some patients are hyperammonemic and have elevated urine organic acids. In between such episodes patients are typically normal (Brown et al. 2001; Gobin et al. 2002; Bonnefont et al. 2004; Bennett and Santani 2016).

Women who are pregnant with a fetus with CPT1A deficiency may present with HELLP-like syndrome, acute fatty liver of pregnancy (AFLP), hypoglycemia, abnormal liver enzymes, and/or hyperammonemia (Bonnefont et al. 2004; Bennett and Santani 2016).

Genetics

Carnitine palmitoyltransferase 1A deficiency is an autosomal recessive disorder, and CPT1A is the only gene that is known to be involved. CPT1A deficiency is a relatively rare disorder, with ~40 pathogenic variants reported to date. The majority of pathogenic variants are missense, though one small in-frame deletion as well as nonsense and other premature termination variants (small insertions, deletions, and splice variants) have also been reported. One gross deletion has been reported (Human Gene Mutation Database). At least three variants have been reported at higher frequencies in specific populations. The p.G710E variant is common among Alaskan and American Hutterites, the p.P497L variant is common among Alaskan Native populations, and the p.K455T variant is common among Finnish patients (Greenberg et al. 2009; Gillingham et al. 2011; Roomets et al. 2012).

The carnitine palmitoyltransferase system is comprised of several proteins with enzyme and transporter functions. These proteins are involved in long-chain fatty acid (LCFA) metabolism, being specifically responsible for the net transport of LCFAs from the cytosol into the mitochondrial matrix. The CPT1 protein is the first component of this system. CPT1 activates LCFAs by catalyzing the transfer of an acyl group to carnitine, which is then transported into the mitochondrial matrix. Multiple isoforms of CPT1 exist. The CPT1A isoform is expressed predominantly in the liver and is the only isoform that has thus far been associated with human disease (Brown et al. 2001; Bonnefont et al. 2004).

Clinical Sensitivity - Sequencing with CNV PGxome

Clinical sensitivity of this test is expected to be high for patients with confirmed carnitine palmitoyltransferase 1A deficiency as, to date, nearly all reported patients have had two pathogenic variants detectable via sequencing. Based on combined results from several studies, 55 pathogenic alleles were identified in 29 affected patients for an overall sensitivity of ~95% (Brown et al. 2001; Gobin et al. 2002; Bennett et al. 2004; Greenberg et al. 2009; Fontaine et al. 2012; Roomets et al. 2012).

Only one gross deletion has been reported in the CPT1A gene (Gobin et al. 2002). Therefore, the sensitivity of duplication/deletion testing for this rare disorder, although not precisely known, is expected to be low.

Testing Strategy

This test provides full coverage of all coding exons of the CPT1A 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

Patients with clinical and biochemical test results consistent with CPT1 deficiency are good candidates for this test. Family members of patients who have known CPT1A mutations are also good candidates. We will also sequence the CPT1A gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
CPT1A 600528
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Carnitine Palmitoyltransferase I Deficiency AR 255120

Citations

  • Bennett M.J. and Santani A.B. 2016. Carnitine Palmitoyltransferase 1A Deficiency. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301700
  • Bennett M.J. et al. 2004. Molecular Genetics and Metabolism. 82: 59-63. PubMed ID: 15110323
  • Bonnefont J.P. et al. 2004. Molecular Aspects of Medicine. 25: 495-520. PubMed ID: 15363638
  • Brown N.F. et al. 2001. Journal of Lipid Research. 42: 1134-42. PubMed ID: 11441142
  • Fontaine M. et al. 2012. JIMD Reports. 6: 7-14. PubMed ID: 23430932
  • Gillingham M.B. et al. 2011. Molecular Genetics and Metabolism. 104: 261-4. PubMed ID: 21763168
  • Gobin S. et al. 2002. Human Genetics. 111: 179-89. PubMed ID: 12189492
  • Greenberg C.R. et al. 2009. Molecular Genetics and Metabolism. 96: 201-7. PubMed ID: 19217814
  • Human Gene Mutation Database (Bio-base).
  • Roomets E. et al. 2012. The Journal of Pediatrics. 160: 473-479.e1. PubMed ID: 21962599

Ordering/Specimens

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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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