Inborn Errors of Metabolism
CPT2 Gene Sequencing

CPT2 Gene Sequencing (CPT2 deficiency)

Gene Tested



Carnitine Palmitoyltransferase II (CPT II) Deficiency


CPT II deficiency is a disorder of long-chain fatty acid oxidation which may result in either of three distinct presentations based upon the affected individual’s age and body systems affected. The infantile / neonatal (hepatocardiomuscular) form typically presents before one year of age with hypoketotic hypoglycemia, acute liver failure, cardiomyopathy, and/or sudden death, triggered by fasting or fever. 

 A more severe neonatal form of CPT II deficiency, including dysmorphic features, brain dysplasia, respiratory distress, hypoglycemia, cardiomegaly, heart rhythm disorders, cystic renal dysplasia, hepatomegaly, and neonatal death, has also been described. 

The adult (myopathic) form typically presents in young adults as episodes of muscle pain, weakness, and rhabdomyolysis triggered by prolonged exercise, or occasionally by illness or fasting. Complications which may arise from the rhabdomyolysis are acute renal failure, respiratory insufficiency, and paroxysmal arrhythmias. In the intervals between episodes, individuals with the classical adult CPT II deficiency appear healthy. Males are more likely to be affected than females. CPT II deficiency is caused by pathogenic variants in the CPT2 gene, and this condition is inherited in an autosomal recessive manner.


• Confirmation of diagnosis in a symptomatic individual 
• Abnormal newborn screen or acylcarnitine profile suggesting CPT II deficiency 

Testing Methodology

PCR-based sequencing of entire coding region, intron/exon boundaries, as well as known pathogenic variants (HGMD 2017.3) in the promoter and deep intronic regions of the specified gene(s).

Sensitivity and Limitations

PCR-based sequencing of the CPT2 gene detects pathogenic variants in >95% of patients with CPT II deficiency. The analytical sensitivity of DNA sequencing is over 99% for the detection of nucleotide base changes, small deletions and insertions in the regions analyzed. Variants in regulatory regions and non-reported variants in untranslated regions may not be detected by this test. Large deletions/ duplications, large insertions and other complex genetic events will not be identified using sequencing methodology.

Turn-Around Time

7 days

CPT Codes

CPT2 full gene sequence analysis: 81404
CPT2 family specific variant analysis: 81403

How to Order

Testing for this gene is also available as part the Metaboseq panel by next-generation sequencing and the Elevated C16 Gene Sequencing panel by Sanger sequencing, which also includes the SLC25A20 gene. Deletion/duplication analysis and targeted variant analysis is also available for this gene. Download Inborn Errors of Metabolism requisition.


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Bonnefont, J. P., F. Taroni, et al. (1996). Molecular analysis of carnitine palmitoyltransferase II deficiency with hepatocardiomuscular expression. Am J Hum Genet 58(5): 971-978.

Illsinger, S., T. Lucke, et al. (2008). Carnitine-palmitoyltransferase 2 deficiency: novel mutations and relevance of newborn screening. Am J Med Genet A 146A(22): 2925-2928.

Joshi PR., et al. (2014) Carnitine palmitoyltransferase II (CPT II) deficiency: genotype-phenotype analysis of 50 patients. J Neurol Sci. 2014 Mar 15;338(1-2):107-11.

Orngreen, M. C., M. Duno, et al. (2005). Fuel utilization in subjects with carnitine palmitoyltransferase 2 gene mutations. Ann Neurol 57(1): 60-66.

Spiekerkoetter, U. (2010). Mitochondrial fatty acid oxidation disorders: clinical presentation of long-chain fatty acid oxidation defects before and after newborn screening. J Inherit Metab Dis 33(5): 527-532.

Taroni, F., E. Verderio, et al. (1993). Identification of a common mutation in the carnitine palmitoyltransferase II gene in familial recurrent myoglobinuria patients. Nat Genet 4(3): 314-320.

Wieser, T. (2004; updated 2011). Carnitine Palmitoyltransferase II Deficiency. GeneReviews. R. A. Pagon, T. D. Bird, C. R. Dolan, K. Stephens and M. P. Adam. Seattle (WA).