Systemic Primary Carnitine Deficiency via the SLC22A5 Gene

Systemic primary carnitine deficiency (SPCD) is a disorder caused by defective carnitine transport from the blood into cells (Shinawi and Abu-Elheiga 2015). The clinical spectrum and age of onset of SPCD is very broad, with variation in presentation even among family members (Shinawi and Abu-Elheiga 2015; El-Hattab 2016). Presentation is thought to be influenced by non-genetic factors, such as diet and illness (Rose et al. 2012).

Initial reports of SPCD were based on symptomatic patients with two different types of clinical presentation. The first group of patients present in infancy or early childhood, typically between 3 months and 2 years of age. These patients have episodic metabolic decompensation associated with hypoketotic hypoglycemia, poor feeding and failure to thrive, irritability, lethargy, hepatomegaly, elevated liver transaminases, and hyperammonemia. Episodes are typically triggered by fasting or illness. The second group of patients present a bit later in childhood, typically between 2 to 4 years of age, with myopathy that involves the skeletal and heart muscle (Shinawi and Abu-Elheiga 2015; El-Hattab 2016).

Newer reports have shown that some adults who present with easy fatigability may have SPCD, and that this disorder may also present as pregnancy-related decrease in stamina or exacerbation of a cardiac arrhythmia. Furthermore, it should be noted that maternal carnitine levels affect fetal carnitine levels. As a result, newborn screening sometimes identifies unaffected neonates with low carnitine levels as a result of being born to an affected, but often clinically asymptomatic or very mildly affected, mother with previously undiagnosed SPCD. Other individuals identified via newborn screening may have SPCD themselves. Based on these findings, it is recommended that follow up testing for both the newborn and mother be considered in cases with positive newborn screening results (Li et al. 2010; Shinawi and Abu-Elheiga 2015; El-Hattab 2016).

Laboratory analysis shows greatly reduced plasma carnitine levels and urinary carnitine wasting in affected individuals. Analysis of fibroblast cell culture should also reveal decreased carnitine transport. In addition, acylcarnitine profiling may fail in affected individuals due to the low level of total carnitine. Treatment for affected individuals is typically administration of oral carnitine and management of symptoms that may occur as a result of the disorder. Early treatment may prevent many symptoms and long-term complications, and thus it is important to identify individuals with SPCD early (Shinawi and Abu-Elheiga 2015; El-Hattab 2016).

SPCD is a rare autosomal recessive disorder that results due to biallelic pathogenic variants in the SLC22A5 gene. The prevalence generally ranges from ~1:20,000 to 1:120,000 depending on the population, though it is particularly prevalent in the Faroe Islands with ~1:300 individuals being affected (El-Hattab 2016). Over 100 pathogenic variants in the SLC22A5 gene have been reported to date. Approximately 60% of the pathogenic variants are missense and ~35% are nonsense or frameshift variants (Human Gene Mutation Database). In addition, several gross deletions have been reported (Lamhonwah and Tein 1998; Li et al. 2010; Roussel et al. 2016). Certain variants have been found to be prevalent in specific populations. These include p.Arg254* in the Chinese population (Tang et al. 2002; Han et al. 2014), p.Arg282* in Whites (Burwinkel et al. 1999; Han et al. 2014) and p.Asn32Ser in the Faroe Islands (Rasmussen et al. 2014).

Although there is not a strict genotype-phenotype correlation, it has been reported that nonsense or frameshift variants are more prevalent amongst groups of symptomatic patients and missense variants are more prevalent in asymptomatic patients. In addition, symptomatic patients have been reported to have lower plasma carnitine levels than asymptomatic patients (Rose et al. 2012; El-Hattab 2016).

The SLC22A5 gene encodes the organic cation transporter 2 protein (OCTN2), which is a high-affinity, sodium-dependent transporter required for the passage of carnitine from the plasma into cells. The OCTN2 protein is found in the kidneys, myocardium, skeletal muscle, placenta and parts of the brain. In addition to transporting carnitine from the plasma, it is also required for renal tubular carnitine reabsorption. Thus, patients with a defective or absent OCTN2 transporter have impaired transport of carnitine from the plasma and also massive urinary wasting of carnitine due to impaired reabsorption in the kidneys (Shinawi and Abu-Elheiga 2015).

Different detection rates of SLC22A5 variants have been reported based on different patient identification methods. In one study, ~70% of 70 infants identified based on a positive newborn screen were found to have at least one SLC22A5 variant. In the same study, ~27% of 52 patients identified based on clinical presentation were found to have at least one SLC22A5 variant (Li et al. 2010). However, in studies of patients with more in-depth biochemical analyses or cellularly confirmed carnitine transport deficiency the detection rate is higher. For example, Rose et al. (2012) reported 54 alleles in 28 individuals, while Han et al. (2014) reported 39 alleles in 20 patients. Based on these studies, clinical sensitivity would be estimated at ~96-98% in patients with confirmed systemic primary carnitine deficiency (SPCD).

While gross deletions and duplications do not appear to be a major cause of systemic primary carnitine deficiency (SPCD), several large deletions in the SLC22A5 gene have been reported (Human Gene Mutation Database). For example, Li et al. (2010) screened a group of 26 patients for SLC22A5 copy number variants. The group tested included 25 patients with a single SLC22A5 variant identified via DNA sequencing and 1 patient who was apparently homozygous for a missense variant. Of this group, one heterozygous gross deletion was detected.

This test provides full coverage of all coding exons of the SLC22A5 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).

In addition to the regions described above, this testing includes coverage for the reported pathogenic intronic c.825-52G>A variant.

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).