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Low Levels of Free Carnitine (C0) via the SLC22A5 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
SLC22A5 81405 81405,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
16039SLC22A581405 81405,81479 $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).

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

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).

Clinical Sensitivity - Sequencing with CNV PGxome

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.

Testing Strategy

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).

Indications for Test

Patients with low levels of free carnitine detected during newborn screen as well as those with clinical and biochemical test results consistent with SPCD are good candidates for this test. Family members of patients who have known SLC22A5 pathogenic variants are also good candidates. We will also sequence the SLC22A5 gene to determine carrier status.


Official Gene Symbol OMIM ID
SLC22A5 603377
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Systemic Carnitine Deficiency AR 212140

Related Test

Systemic Primary Carnitine Deficiency via the SLC22A5 Gene


  • Burwinkel et al. 1999. PubMed ID: 10425211
  • El-Hattab et al. 2016. PubMed ID: 22420015
  • Han et al. 2014. PubMed ID: 25132046
  • https://www.babysfirsttest.org/newborn-screening/states
  • https://www.cdc.gov/newbornscreening/
  • https://www.hrsa.gov/advisory-committees/heritable-disorders/rusp
  • Human Gene Mutation Database (Biobase).
  • Lamhonwah and Tein. 1998. PubMed ID: 9826541
  • Li et al. 2010. PubMed ID: 20574985
  • Rasmussen et al. 2014. PubMed ID: 23963628
  • Rose et al. 2012. PubMed ID: 21922592
  • Roussel et al. 2016. PubMed ID: 26190315
  • Shinawi M.S. and Abu-Elheiga L.A. 2015. Fatty Acid Metabolism and Defects. In: Lee B. and Scaglia F., editors. Inborn Errors of Metabolism: From Neonatal Screening to Metabolic Pathways. New York: Oxford University Press, p 152-179.
  • Tang et al. 2002. PubMed ID: 12204000
  • Watson et al. 2006 PubMed ID: 16783161


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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