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Carnitine Palmitoyltransferase II Deficiency via the CPT2 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
CPT2 81404 81404,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9563CPT281404 81404,81479 $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


  • Maxime Cadieux-Dion, PhD

Clinical Features and Genetics

Clinical Features

Carnitine palmitoyltransferase II (CPT II) deficiency is one of the most commonly inherited disorders of long-chain fatty acid oxidation (Corti et al. 2008). Three types of CPT II deficiency have been reported.

CPT II deficiency Types I and II are rare, severe disorders that involve multiple body systems. Patients present with recurrent attacks of acute liver failure with hypoketotic hypoglycemia, respiratory distress, lethargy, vomiting, seizures, transient hepatomegaly, and possibly coma. Cardiac involvement, including cardiomyopathy and cardiac arrhythmias that can lead to sudden death, is observed in about half of the affected patients. These forms of CPT II deficiency are associated with enzyme activity levels <10% of control. Biochemically, patients may be observed to have low levels of free and total carnitine, metabolic acidosis, and hyperammonemia.

Type II is classified as severe infantile CPT II deficiency, and is also referred to as the hepatocardiomuscular form. Onset for Type II patients is typically within the first year of life, with fatality being most common during the time period from ~3-18 months of age (Illsinger et al. 2008).

Type I CPT II deficiency is classified as the lethal neonatal form and presents within the first few days of life. In addition to the clinical features observed in type II patients, type I CPT II deficient patients are typically observed to have dysmorphic features, such as facial abnormalities and malformations of the kidneys and brain (Bonnefont et al. 2004; Corti et al. 2008; Wieser 2017).

Type III CPT II deficiency is the most common. This form is primarily a myopathic disorder. Onset occurs from childhood through late adulthood, though is most commonly observed between the ages of 6 and 20 years (Bonnefont et al. 2004). Symptoms include episodic attacks of myalgia and muscle stiffness or weakness, rhabdomyolysis and myoglobinuria. Creatine kinase (CK) and transaminase levels may be elevated during attacks, while carnitine levels may be decreased or normal. Muscle lipid storage has been observed in approximately 20% of patients. A variety of stressors may trigger an attack, such as prolonged exercise, fasting, exposure to extreme temperatures, viral infection, fever, emotional stress, or exposure to anesthesia or other drugs. Between attacks, patients are typically clinically normal. For reasons that are not understood, males are much more likely to be affected than females (Bonnefont et al. 2004; Corti et al. 2008; Wieser 2017).

Laboratory analysis in affected patients may reveal elevated C12 to C18 acylcarnitines, especially C16 and C18:1. Patients with glutaric aciduria type II and carnitine-acylcarnitine translocase deficiency may also have a similar acylcarnitine profile, though other biochemical abnormalities may help to differentiate between these disorders (Wieser 2017).


CPT II deficiency is primarily an autosomal recessive disorder, although a few manifesting heterozygotes have been reported (Wieser 2017). The CPT2 gene is the only gene that is known to be involved. Approximately 100 pathogenic variants in the CPT2 gene have been reported to date. Approximately two-thirds of the pathogenic variants are missense, with the remainder being small frameshift deletions, insertions and splice variants (Anichini et al. 2011; Human Gene Mutation Database).

Several variants have been commonly reported to be associated with the myopathic form (type III) of CPT II deficiency: p.Ser113Leu (accounts for ~60-70% of alleles in Whites), p.Lys414Thrfs*7 (~20%), p.Pro50His, p.Arg503Cys, p.Gly549Asp, and p.Met214Thr (~15% together) (Deschauer et al. 2005; Fanin et al. 2012; Joshi et al. 2014; Wieser 2017). In general, the severe infantile and lethal neonatal forms are associated with variants expected to have a severe effect on the protein, such as p.Lys414Thrfs*7 (Wieser 2017). It has been noted that for most patients with the myopathic form, at least one pathogenic variant resides within exons 1 through 3, whereas patients with the infantile or neonatal forms typically have two pathogenic variants located in exons 4 or 5 (Bonnefont et al. 2004). There is some level of genotype-phenotype correlation, with myopathic patients typically carrying variants that have a less severe effect on the CPT II protein, while patients with the infantile or neonatal forms usually have at least one severe, null variant (Corti et al. 2008; Isackson et al. 2008). However, this is not always the case, as some variants have been observed in patients with different types of CPT II deficiency, such as p.Lys414Thrfs*7 (Wieser 2017).

The carnitine palmitoyltransferase system is a set of 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 CPT II protein is located within the mitochondrial matrix where it is associated with the inner mitochondrial membrane. The CPT II protein converts acyl-carnitines that were transported into the mitochondrial matrix back to acyl-CoA molecules, which are then available for β-oxidation (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 II deficiency as, to date, nearly all reported patients have had two pathogenic variants detectable via direct CPT2 sequencing. Based on combined results from several studies, 296 alleles have been reported in 154 patients, for a sensitivity of ~96% (Deschauer et al. 2005; Corti et al. 2008; Isackson et al. 2008; Fanin et al. 2012; Joshi et al. 2014).

To date, no gross deletions or duplications have been reported in the CPT2 gene (Human Gene Mutation Database). Therefore, the sensitivity of duplication/deletion testing for this rare disorder, although not precisely known, is low.

Testing Strategy

This test provides full coverage of all coding exons of the CPT2 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 CPT II deficiency are good candidates for this test. Family members of patients who have known CPT2 pathogenic variants are also good candidates. We will also sequence the CPT2 gene to determine carrier status.


Official Gene Symbol OMIM ID
CPT2 600650
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Anichini A. et al. 2011. Neurological Research. 33: 24-32. PubMed ID: 20810031
  • Bonnefont J.P. et al. 2004. Molecular Aspects of Medicine. 25: 495-520. PubMed ID: 15363638
  • Corti S. et al. 2008. Journal of the Neurological Sciences. 266: 97-103. PubMed ID: 17936304
  • Deschauer M. et al. 2005. Archives of Neurology. 62: 37-41. PubMed ID: 15642848
  • Fanin M. et al. 2012. Clinical Genetics. 82: 232-9. PubMed ID: 21913903
  • Human Gene Mutation Database (Bio-base).
  • Illsinger S. et al. 2008. American Journal of Medical Genetics. Part A. 146A: 2925-8. PubMed ID: 18925671
  • Isackson P.J. et al. 2008. Molecular Genetics and Metabolism. 94: 422-7. PubMed ID: 18550408
  • Joshi P.R. et al. 2014. Journal of the Neurological Sciences. 338: 107-11. PubMed ID: 24398345
  • Wieser T. 2017. Carnitine Palmitoyltransferase II 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: 20301431


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