Glycogen Storage Disease Type IX via the PHKA1 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 | |
|---|---|---|---|---|---|
| 11851 | PHKA1 | 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. Defects in the muscle alpha subunit of Phk (OMIM 300559) are a rare cause of GSD. Only a handful of patients have been described in the literature (Wehner et al. Hum Mol Genet 3:1983-1987, 1994). The clinical features of muscle Phk deficiency are generally similar to GSD Types V and VII. Onset can be in childhood or adult life. Symptoms include exercise intolerance, muscle cramps, muscle glycogen accumulation, and in some patients, progressive muscle weakness. The heart and liver do not appear to be involved. Liver and erythrocyte Phk activity is normal.
Genetics
The PHKA1 gene encodes the muscle alpha subunit of Phk. PHKA1 variants are inherited in an X-linked recessive fashion. All affected individuals reported to date have been male. Four causative variants in PHKA1 have been reported. These variants were missense, nonsense, frameshift, and splicing (Wehner et al. 1994; Burwinkel et al. Eur J Hum Genet 11:516-526, 2003; Wuyts et al. Am J Med Genet 133A:82-84, 2005).
Clinical Sensitivity - Sequencing with CNV PGxome
Little is known about the sensitivity of this test. Burwinkel et al. 2003 reported finding a causative variant in 1 out of 6 patients.
Testing Strategy
This test provides full coverage of all coding exons of the PHKA1 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 male patients with features of muscle Phk deficiency and with family history consistent with X-linked recessive inheritance. Male patients who are negative for GSD type V (PYGM gene) and GSD type VII (PFKM gene) tests may also be good candidates for this test. Female patients with two causative variants in PHKA1 are conceivable but should nearly always have affected fathers. Patients with common features of liver involvement such as hepatomegaly, growth retardation, and elevated liver glycogen are not good candidates for this test.
Candidates for this test are male patients with features of muscle Phk deficiency and with family history consistent with X-linked recessive inheritance. Male patients who are negative for GSD type V (PYGM gene) and GSD type VII (PFKM gene) tests may also be good candidates for this test. Female patients with two causative variants in PHKA1 are conceivable but should nearly always have affected fathers. Patients with common features of liver involvement such as hepatomegaly, growth retardation, and elevated liver glycogen are not good candidates for this test.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| PHKA1 | 311870 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Glycogen Storage Disease Type IXd | XL | 300559 |
Citations
- Burwinkel, B., et.al. (2003). "Muscle glycogenosis with low phosphorylase kinase activity: mutations in PHKA1, PHKG1 or six other candidate genes explain only a minority of cases." Eur J Hum Genet 11(7): 516-26. PubMed ID: 12825073
- Wehner, M., et.al. (1994). "Human muscle glycogenosis due to phosphorylase kinase deficiency associated with a nonsense mutation in the muscle isoform of the alpha subunit." Hum Mol Genet 3(11): 1983-7. PubMed ID: 7874115
- Wuyts, W., et.al. (2005). "Myopathy and phosphorylase kinase deficiency caused by a mutation in the PHKA1 gene." Am J Med Genet A 133A(1): 82-4. PubMed ID: 15637709
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.