Carnitine Palmitoyltransferase II Deficiency via the CPT2 Gene

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 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.

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).