• Test code: 06103
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)
  • Alternate specimens:
    Saliva, assisted saliva, buccal swab and gDNA
  • Sample requirements
  • Request a sample kit

Invitae Low C0 Test

Test description

The Invitae Low C0 Test analyzes the SLC22A5 gene, which is associated with low C0 (free carnitine) on newborn screening (NBS), plasma acylcarnitine analysis, and total and free carnitine in plasma. Genetic testing of this gene may confirm a diagnosis and help guide treatment and management decisions.

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Primary panel (1 gene)

Alternative tests to consider

The Invitae Fatty Acid Oxidation Defects Panel has been designed to provide a broad genetic analysis of this class of disorders. Depending on the individual’s clinical and family history, this broader panel may be appropriate. It can be ordered at no additional cost.

  • primary carnitine deficiency

Low C0 (free carnitine) may be detected during newborn screening, acylcarnitine analysis, and total and free carnitine in plasma due to primary carnitine deficiency or secondary carnitine deficiency. Secondary carnitine deficiency can be caused both by genetic causes (other fatty acid oxidation disorders, organic acidemias) and by non-genetic causes (e.g., malnutrition, prematurity). Patients with primary carnitine deficiency may be differentiated from genetic causes of secondary carnitine deficiency through characteristic elevations of acylcarnitine species and possibly organic acids for these disorders. In patients with secondary carnitine deficiency due to non-genetic causes, characteristic elevation of free carnitine in urine will not be present. Healthy babies with abnormal newborn screening for low C0 may also be picked up due to maternal primary carnitine deficiency.

Patients with primary carnitine deficiency show a range in severity and may present in the infantile period (three months to two years), early childhood (two to four years), or as an adult, or they may be asymptomatic. Patients with the infantile-onset form have the typical metabolic features of a fatty acid oxidation disorder: poor feeding, irritability, lethargy, hepatomegaly, hypoketotic hypoglycemia, hyperammonemia, and elevated liver transaminases. Prolonged fasting or intercurrent illness may precipitate bouts of metabolic decompensation in these patients.

Patients with the childhood-onset form have a myopathic presentation that may include hypotonia, dilated cardiomyopathy, skeletal muscle myopathy, and elevated creatine kinase. Patients with this myopathic form are at risk of sudden cardiac death. Adult females have been detected through abnormal newborn screening findings in their babies. Roughly half of these adult patients have clinical symptoms and half are asymptomatic, despite having low carnitine. The most common symptom is fatigue, though cardiomyopathy and arrhythmias have been reported.

Carnitine supplementation is used to treat patients with primary carnitine deficiency. Emergency protocols are also implemented during times of metabolic crises, most commonly caused by illness, infection, or prolonged periods of fasting; if left untreated, it can lead to coma and death. On continued carnitine supplementation, patients have a good prognosis, so early diagnosis and detection may improve the long-term outcome of these patients.

For patients with biochemical features that are consistent with primary carnitine deficiency (low free, total, and acylcarnitine fractions in plasma or serum with elevated free carnitine in urine), greater than 70% will have two pathogenic variants in SLC22A5.

Primary carnitine deficiency is inherited in an autosomal recessive manner.

The prevalence of low C0 is dependent on laboratory cutoffs and ethnicity. The overall prevalence of confirmed primary carnitine deficiency has been estimated at 1 in 55,500, though it can be as high as 1 in 5,500 in some ethnic populations.

This test may be appropriate for patients:

  • with low C0 on newborn screening, plasma acylcarnitines, or total and free carnitine analysis
  • with elevated free carnitine in urine on a sample taken prior to the commencement of carnitine supplementation

For considerations for testing please refer to:

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
SLC22A5 NM_003060.3