Glycogen Storage Disease Type IX via the PHKA2 Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 11853 | PHKA2 | 81479 | 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.
Clinical Features and Genetics
Clinical Features
Glycogen storage disease (GSD) resulting from glycogen phosphorylase kinase deficiency (sometimes called GSD type IX) has several subtypes. This is because the phosphorylase kinase (Phk) enzyme is comprised of four subunits (αβγδ) and because there are tissue-specific forms of the subunits. GSD type IX is one of the most common types of GSD, involving ~25% of all GSD patients (Burwinkel et al. Hum Genet 102:423-429, 1998; Hendrickx et al. Am J Hum Genet 64:1541-1549, 1999). Defects in the liver alpha subunit of Phk (OMIM 306000) are by far the most common cause (~75%) of GSD type IX. Patients typically present in the first few months of life with hepatomegaly, growth retardation, elevated liver glycogen, and elevated serum triglycerides and cholesterol.
Genetics
The PHKA2 gene encodes the liver alpha subunit of Phk. PHKA2 variants are inherited in an X-linked recessive fashion. Nearly all affected individuals are male. About 50 causative PHKA2 missense, nonsense, in-frame deletion, frameshift and splicing variants have been reported (Burwinkel et al. 1998; Hendrickx et al. 1999; Beauchamp et al. Molec Genet Metab 92:88-99, 2007). Causative variants are located throughout the length of the gene; no variants are predominant. Patients with missense variants may have normal or even elevated erythrocyte Phk activity (but reduced liver Phk activity). At least one multi-exon deletion has been reported (Fukao et al. Molec Genet Metab 92:179-182, 2007).
Clinical Sensitivity - Sequencing with CNV PGxome
Sensitivity of this test has not been reported.
Testing Strategy
This test provides full coverage of all coding exons of the PHKA2 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 are all patients with symptoms of GSD type IX and with family history consistent with X-linked recessive inheritance. Male patients with deficiencies in phosphorylase kinase activity are also good candidates.
Candidates for this test are all patients with symptoms of GSD type IX and with family history consistent with X-linked recessive inheritance. Male patients with deficiencies in phosphorylase kinase activity are also good candidates.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| PHKA2 | 300798 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Glycogen Storage Disease Type IXa1 | XL | 306000 |
Citations
- Beauchamp, N. J., et.al. (2007). "Glycogen storage disease type IX: High variability in clinical phenotype." Mol Genet Metab 92(1-2): 88-99. PubMed ID: 17689125
- Burwinkel, B., et.al. (1998). "Variability of biochemical and clinical phenotype in X-linked liver glycogenosis with mutations in the phosphorylase kinase PHKA2 gene." Hum Genet 102(4): 423-9. PubMed ID: 9600238
- Fukao, T., et.al. (2007). "Identification of Alu-mediated, large deletion-spanning introns 19-26 in PHKA2 in a patient with X-linked liver glycogenosis (hepatic phosphorylase kinase deficiency)." Mol Genet Metab 92(1-2): 179-82. PubMed ID: 17581768
- Hendrickx, J., et.al. (1999). "Complete genomic structure and mutational spectrum of PHKA2 in patients with x-linked liver glycogenosis type I and II." Am J Hum Genet 64(6): 1541-9. PubMed ID: 10330341
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
View Ordering Instructions1) Select Test Type
2) Select Additional Test Options
No Additional Test Options are available for this test.