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Spastic Paraplegia 46 via the GBA2 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
5425 GBA2 81479 81479,81479 $990 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
5425GBA281479 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.

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

  • Greg Fischer, PhD

Clinical Features and Genetics

Clinical Features

Spastic Paraplegia 46 (SPG46) is a type of hereditary spastic paraplegia (HSP) characterized by early onset (1-20 years, median 7 years) of slowly progressive muscle stiffness and weakness and cerebellar signs. Some SPG46 patients may also have cognitive impairment, bladder dysfunction, cataract, and cerebral and corpus callosum atrophy on brain imaging (Boukhris et al. 2010; Martin et al. 2013; van de Warrenburg et al. 2016). Most SPG46 patients will need a cane in their 20s and become wheelchair-bound within 20-25 years of disease onset (Votsi et al. 2014).

Genetics

SPG46 is inherited in an autosomal recessive (AR) manner. This disorder is caused by homozygous or compound heterozygous pathogenic variants in the GBA2 gene (Hammer et al. 2013; Sultana et al. 2015). To date, different types of variants (missense, nonsense, splicing and frameshift deletions/duplications) have been found in GBA2 to cause SPG46 (Human Gene Mutation Database). GBA2 encodes the enzyme non-lysosomal glucosylceramidase, which is localized at the cell surface and in the endoplasmic reticulum (Matern et al. 2001). The exact disease mechanism is still not clear; however the loss of function of glucocerebrosidase GBA2 is believed to impair the formation of motor neuron axons in SPG46 patients (Martin et al. 2013).

Clinical Sensitivity - Sequencing with CNV PGxome

It is difficult to estimate the exact clinical sensitivity of this test due to the lack of large cohort studies. All the pathogenic variants in the GBA2 gene reported to date can be detected by sequencing.

Testing Strategy

This test provides full coverage of all coding exons of the GBA2 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 symptoms consistent with AR HSP may consider this test. Testing is also indicated for family members of patients who have known GBA2 pathogenic variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in GBA2.

Gene

Official Gene Symbol OMIM ID
GBA2 609471
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Spastic Paraplegia 46 AR 614409

Citations

  • Boukhris A. et al. 2010. Neurogenetics. 11: 441-8. PubMed ID: 20593214
  • Hammer M.B. et al. 2013. American Journal of Human Genetics. 92: 245-51. PubMed ID: 23332917
  • Human Gene Mutation Database (Bio-base).
  • Martin E. et al. 2013. American Journal of Human Genetics. 92: 238-44. PubMed ID: 23332916
  • Matern H. et al. 2001. The Journal of Biological Chemistry. 276: 37929-33. PubMed ID: 11489889
  • Sultana S. et al. 2015. Biochemical and Biophysical Research Communications. 465: 35-40. PubMed ID: 26220345
  • van de Warrenburg B.P. et al. 2016. European Journal of Human Genetics. 24: 1460-6. PubMed ID: 27165006
  • Votsi C. et al. 2014. Annals of Human Genetics. 78: 13-22. PubMed ID: 24252062

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

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View Ordering Instructions

1) Select Test Method (Platform)


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.
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