Glycogen Storage Disease Type IX via the PHKB 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 | |
|---|---|---|---|---|---|
| 11855 | PHKB | 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 genetic causes. 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 (Hendrickx et al. Am J Hum Genet 64:1541-1549, 1999). Patients typically present in the first few months of life with hepatomegaly, growth retardation, elevated liver or muscle glycogen, and elevated serum triglycerides and cholesterol. In some patients, symptoms gradually subside with age, while in others cirrhosis develops.
Genetics
The PHKB gene on chromosome 16 encodes the β subunit of the phosphorylase kinase enzyme. GSD type IX due to PHKB variants (OMIM 261750) is an autosomal recessive disorder (there are also X-linked recessive forms). Nearly all of the ~15 reported pathogenic PHKB variants have been nonsense, frameshift or splicing (Burwinkel et al. Hum Mol Genet 6:1109-1115, 1997; van den Berg et al. Am J Hum Genet 61:539-546, 1997; Beauchamp et al. Mol Genet Metab 92:88-99, 2007). One larger intragenic deletion has been reported (Burwinkel et al. 1997). Some residual Phk enzyme activity may remain even after complete loss of functional PHKB protein. PHKB variants have not been found in patients with only muscle disease and no liver involvement (Burwinkel et al. Eur J Hum Genet 11:516-526, 2003).
Clinical Sensitivity - Sequencing with CNV PGxome
Out of 12 GSD Type IX families, Beauchamp et al. (2007) reported eight with variants in the PHKA2 gene, two with variants in the PHKG2 gene, and one or two with variants in the PHKB gene.
Testing Strategy
This test provides full coverage of all coding exons of the PHKB 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
Patients with clinical features of (liver) GSD type IX and patients with Phk deficiency are candidates for this test. Female patients, male patients with negative results for PHKA2, or male patients with consanguineous parents are preferred candidates. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PHKB.
Patients with clinical features of (liver) GSD type IX and patients with Phk deficiency are candidates for this test. Female patients, male patients with negative results for PHKA2, or male patients with consanguineous parents are preferred candidates. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PHKB.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| PHKB | 172490 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Glycogen Storage DiseaseType IXb | AR | 261750 |
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. (1997). "Autosomal glycogenosis of liver and muscle due to phosphorylase kinase deficiency is caused by mutations in the phosphorylase kinase beta subunit (PHKB)." Hum Mol Genet 6(7): 1109-15. PubMed ID: 9215682
- 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
- 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
- van den Berg, I. E., et.al. (1997). "Autosomal recessive phosphorylase kinase deficiency in liver, caused by mutations in the gene encoding the beta subunit (PHKB)." Am J Hum Genet 61(3): 539-46. PubMed ID: 9326319
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.