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Mitochondrial Phosphoenolpyruvate Carboxykinase 2 Deficiency via the PCK2 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
PCK2 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8247PCK281479 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • McKenna Kyriss, PhD

Clinical Features and Genetics

Clinical Features

Patients with mitochondrial diseases or other diseases that mimic mitochondrial diseases present with a wide variety of phenotypes and age of onset, making diagnosis of these disorders challenging (DaRe et al. 2013). Clinical features can include encephalomyopathy, combinations of multisystemic symptoms affecting at least three organ symptoms, and a progressive clinical course with episodes of worsening symptoms. Enzymology studies reveal decreased respiratory chain complex (RCC) activity, and metabolic studies may show at least one indicator of impaired RCC activity. Additional diagnostic criteria are described by Bernier et al. (2002).

Disorders of phosphoenolpyruvate carboxykinase (PEPCK) are thought to be a rare cause of childhood onset lactic acidemia. In humans, two PEPCK isozymes are found. One is located in the mitochodria and is encoded by the PCK2 gene. The second is found in the cytosol and is encoded by the PCK1 gene (Robinson 2014). A few early reports have described children with lactic acidemia, hypoglycemia, hypotonia, hepatomegaly and failure to thrive who were also found to have decreased PEPCK enzyme activity (Robinson 2014). More recently, a single PEPCK deficient patient was identified as part of a study of individuals diagnosed with or suspected of having a mitochondrial disorder. A large Next Generation sequencing panel of 447 genes was used in attempt to diagnose these patients (DaRe et al. 2013). This particular patient was found to be a compound heterozygote for two variants in the PCK2 gene, which encodes the mitochondrial PEPCK isozyme. This patient was reported to have abnormal RCC activity and/or muscle pathology, in addition to clinical symptoms consistent with a mitochondrial disorder (DaRe et al. 2013).

Genetics

Mitochondrial PEPCK deficiency is thought to be inherited in an autosomal recessive manner, and is caused by pathogenic variants in the PCK2 gene (DaRe et al. 2013). To date, only missense causative variants have been reported in the PCK2 gene.

The PCK2 gene is a nuclear encoded gene containing 10 coding exons and located on chromosome 14 (14q11-q12). The PEPCK enzyme plays a critical role in gluconeogenesis by catalyzing the conversion of oxaloacetate to phosphoenolpyruvate. The PCK2 gene is expressed primarily in the pancreas, kidney and liver (Modaressi et al. 1998).

Clinical Sensitivity - Sequencing with CNV PGxome

Clinical sensitivity cannot be estimated because only a single patient has been reported (DaRe et al. 2013; Robinson 2014). Analytical sensitivity may be high because all reported pathogenic variants are detectable by sequencing.

To date, no large deletions or duplications have been described in the PCK2 gene.

Testing Strategy

This test provides full coverage of all coding exons of the PCK2 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

Individuals with a suspected mitochondrial disorder and lactic acidemia are good candidates for this test, particularly if other causes of disease have been ruled out. Family members of patients who have known PCK2 variants are also good candidates. We will sequence the PCK2 gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
PCK2 614095
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
Cytosolic Phosphoenolpyruvate Carboxykinase 1 Deficiency via the PCK1 Gene

Citations

  • Bernier F.P. et al. 2002. Neurology. 59: 1406-11.  PubMed ID: 12427892
  • DaRe J.T. et al. 2013. Bmc Medical Genetics. 14: 118.  PubMed ID: 24215330
  • Modaressi S. et al. 1998. The Biochemical Journal. 333 ( Pt 2): 359-66.  PubMed ID: 9657976
  • Robinson B.H. 2014. Lactic Acidemia: Disorders of Pyruvate Carboxylase and Pyruvate Dehydrogenase. Online Metabolic & Molecular Bases of Inherited Disease, New York, NY: McGraw-Hill.

Ordering/Specimens

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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ORDER OPTIONS

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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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