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Mitochondrial Phosphate Carrier Deficiency via the SLC25A3 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
SLC25A3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8485SLC25A381479 81479,81479 $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).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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


  • Kym Bliven, PhD

Clinical Features and Genetics

Clinical Features

Mitochondrial phosphate carrier deficiency is a rare inherited disorder characterized by hypertrophic cardiomyopathy, muscular hypotonia, and lactic acidosis (Seifert et al. 2015; Mayr et al. 2007; Mayr et al. 2011; Bhoj et al. 2015). In contrast to other mitochondrial disorders that cause cardiomyopathy, mitochondrial phosphate carrier deficiency patients retain normal oxidative phosphorylation (OXPHOS) complex activities and do not exhibit neurocognitive involvement.

To date, fewer than ten individuals with this disorder have been reported worldwide. In these patients, the disease was detected during prenatal ultrasound investigation or presented shortly after birth.


Mitochondrial phosphate carrier deficiency is an autosomal recessive disorder caused by defects in the mitochondrial phosphate carrier gene SLC25A3 (Mayr et al. 2007; Mayr et al. 2011). The mitochondrial phosphate carrier (also referred to as PiC) catalyzes the transport of phosphate into the mitochondrial matrix, a porcess that is essential for the aerobic synthesis of adenosine triphosphate (ATP). The SLC25A3 gene has two tissue-specific alternative isoforms, known as PiC-A and PiC-B. Both isoforms have 7 coding exons, although each isoform carries a unique third exon. PiC-A is predominantly found in heart and skeletal muscle; in contrast, PiC-B is ubiquitously expressed, with highest levels in the lung and thyroid (Dolce et al. 1996).

Several causative missense variants, one splicing variant, and one small deletion/insertion have been reported in SLC25A3 to date (Human Gene Mutation Database). Two reported SLC25A3 causative variants (c.215G>A and c.158-9A>G) only affect exon 3A of PiC-A (Mayr et al. 2011). All other reported pathogenic variants may affect both the PiC-A and PiC-B isoforms (Mayr et al. 2007; Bhoj et al. 2015)

Clinical Sensitivity - Sequencing with CNV PGxome

The clinical sensitivity for this test is difficult to estimate, as pathogenic variants in the SLC25A3 gene have been reported in fewer than ten individuals to date (Mayr et al. 2007; Mayr et al. 2011; Bhoj et al. 2015). Analytical sensitivity is expected to be high, however, as all of the pathogenic variants reported in these patients can be detected via sequencing.

No gross deletions or insertions have been reported in the SLC25A3 gene to date (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the SLC25A3 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).

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

Candidates for this test include patients who present with mitochondrial phosphate carrier deficiency. In particular, early-onset hypertrophic cardiomyopathy and lactic acidosis, coupled with normal oxidative phosphorylation (OXPHOS) complex activities during biochemical analysis, has been suggested as an indication for SLC25A3 testing (Mayr et al. 2011). Testing is also indicated for family members of patients with known pathogenic variants in SLC25A3. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SLC25A3.


Official Gene Symbol OMIM ID
SLC25A3 600370
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Mitochondrial Phosphate Carrier Deficiency AR 610773


  • Bhoj E.J. et al. 2015. JIMD Reports. 19:59-66. PubMed ID: 25681081
  • Dolce V. et al. 1996. FEBS Letters. 399:95-8. PubMed ID: 8980128
  • Human Gene Mutation Database (Bio-base).
  • Mayr J.A. et al. 2007. American Journal of Human Genetics. 80:478-84. PubMed ID: 17273968
  • Mayr J.A. et al. 2011. Neuromuscular Disorders. 21:803-8. PubMed ID: 21763135
  • Seifert E.L. et al. 2015. Biochemical and Biophysical Research Communications. 464:369-75. PubMed ID: 26091567


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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View Ordering Instructions

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2) Select Additional Test Options

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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