Cytosolic Phosphoenolpyruvate Carboxykinase 1 Deficiency via the PCK1 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
11849 PCK1 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11849PCK181479 81479(x2) $890 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 backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

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

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days 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

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, two Ashkenazi Jewish siblings were reported to be homozygous for a missense variant in the PCK1 gene (Adams et al. 2014). Both siblings exhibited gross and fine motor delays, intellectual disability, illness-associated lethargy, fasting hypoglycemia, ketonuria, and metabolic acidosis. The stability of the cytosolic PEPCK enzyme was found to be greatly decreased in both siblings.

Genetics

Mitochondrial PEPCK deficiency is thought to be inherited in an autosomal recessive manner, and is caused by pathogenic variants in the PCK1 gene (Adams et al. 2014). To date, only a single missense pathogenic variant has been reported in the PCK1 gene. The PCK1 gene is a nuclear encoded gene containing 9 coding exons and is located on chromosome 20 (20q13.31). The PEPCK enzyme plays a critical role in gluconeogenesis by catalyzing the conversion of oxaloacetate to phosphoenolpyruvate. The PCK1 gene is expressed primarily in the kidney and liver (Modaressi et al. 1998).

Clinical Sensitivity - Sequencing with CNV PGxome

Clinical sensitivity cannot be estimated because only a very small number of patients have been reported (Adams et al. 2014; Robinson 2014). Analytical sensitivity may be high because the only reported pathogenic variant is detectable by sequencing.

To date, no large deletions or duplications have been described in the PCK1 gene.

Testing Strategy

This test provides full coverage of all coding exons of the PCK1 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 lactic acidemia of unknown cause and clinical symptoms suggestive of PEPCK deficiency are good candidates for this test, particularly if other causes of disease have been ruled out. Family members of patients who have known PCK1 variants are also good candidates. We will sequence the PCK1 gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
PCK1 614168
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
Mitochondrial Phosphoenolpyruvate Carboxykinase 2 Deficiency via the PCK2 Gene

Citations

  • Adams D.R. et al. 2014. Molecular Genetics and Metabolism. 113: 161-70.  PubMed ID: 24863970
  • 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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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