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Invitae Citrate Transporter Deficiency Test

Test description

The Invitae Citrate Transporter Deficiency Test analyzes the SLC13A5 gene which encodes a protein responsible for citrate transport. Pathogenic mutations in SLC13A5 cause a form of early infantile epileptic encephalopathy manifested as seizures, global developmental delay, movement disorder and hypotonia. This test is useful for the diagnosis of patients whose clinical symptoms indicate citrate transporter deficiency. Genetic testing of this gene may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant would also guide testing and diagnosis of at-risk relatives.

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Primary panel (1 gene)

Alternative tests to consider

For a broader analysis of the genes associated with early infantile epileptic encephalopathy:

  • citrate transporter deficiency

Citrate transporter deficiency is primarily a neurological disorder associated with pathogenic mutations in the SLC13A5 gene. The citrate transporter exports the TCA cycle intermediates, citrate and isocitrate, from the mitochondria to the cytoplasm where they are utilized in fatty acid and sterol synthesis, and help regulate glycolysis.

Citrate transporter deficiency is an extremely rare condition and affected individuals have been reported with an early infantile epileptic encephalopathy that presents within a few days of life. Additionally, commonly reported symptoms include recurrent respiratory distress, severe global developmental delay, movement disorder and hypotonia. Brain anomalies, facial dysmorphism and premature death have also been reported in affected individuals.

Biochemical abnormalities include elevations of both D-2 and L-2-hydroxyglutaric acids on urine organic acid analysis. Additionally, elevations of Krebs cycle intermediates, and decreased citrate and isocitrate may also be present.

Citrate transporter deficiency is a very rare disorder, clinical sensitivity has not been established (PMID: 24995870).

Citrate transporter deficiency is inherited in an autosomal recessive manner.

Citrate transporter deficiency is a very rare disorder, the prevalence of this condition in the general population is unknown (PMID: 24995870).

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, +/- 10 base pairs of adjacent intronic sequence in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

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
SLC13A5 NM_177550.4