Low Levels of Free Carnitine (C0) via the SLC22A5 Gene

Newborn screening (NBS) tests are performed soon after birth with the goal of identifying individuals that may be affected by certain disorders before disease-related disability or death occurs. Appropriate medical management beginning early in life can prevent all or many symptoms in the affected individuals (Watson et al. 2006 PubMed ID: 16783161; https://www.cdc.gov/newbornscreening/). While NBS is required within all states and territories in the United States, individual state or territory public health departments determine which conditions are included on the NBS panel (https://www.babysfirsttest.org/newborn-screening/states). NBS protocols outside of the United States vary from country to country. At a minimum, all core conditions on the Recommended Uniform Screening Panel (RUSP) should be included on NBS panels within the United States. In addition, NBS testing may also include secondary conditions, which are disorders that can be detected as part of the differential diagnosis of a core condition (https://www.hrsa.gov/advisory-committees/heritable-disorders/rusp). Following an abnormal NBS result, follow up diagnostic testing is indicated. Such testing may include biochemical methodologies (for example, urine organic acid analysis or plasma acylcarnitine analysis), enzyme assays, and/or molecular genetic testing.

This test is designed for individuals with NBS results showing low levels of free carnitine (C0), which can indicate systemic primary carnitine deficiency (SPC). SPC deficiency is a core condition on the RUSP.

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 et al. 2016. PubMed ID: 22420015). 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. PubMed ID: 9826541; Li et al. 2010. PubMed ID: 20574985; Roussel et al. 2016. PubMed ID: 26190315). Certain variants have been found to be prevalent in specific populations. These include p.Arg254* in the Chinese population (Tang et al. 2002. PubMed ID: 12204000; Han et al. 2014. PubMed ID: 25132046), p.Arg282* in White populations (Burwinkel et al. 1999. PubMed ID: 10425211; Han et al. 2014. PubMed ID: 25132046) and p.Asn32Ser in the Faroe Islands (Rasmussen et al. 2014. PubMed ID: 23963628).

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. PubMed ID: 21922592; El-Hattab et al. 2016. PubMed ID: 22420015).

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. PubMed ID: 20574985). 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 with SLC22A5 variants in 28 individuals, while Han et al. (2014) reported 39 alleles with SLC22A5 variants 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) detected one heterozygous gross deletion in a group of 26 patients screened for SLC22A5 copy number variants.

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).