Autosomal Recessive Spinocerebellar Ataxia and Amyotrophic Lateral Sclerosis Type 4 via the SETX Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 3227 | SETX | 81406 | 81406,81479 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
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
Autosomal recessive cerebellar ataxias (ARCAs) are a heterogeneous group of neurological disorders involving both the central and peripheral nervous systems and in some cases, additional systems and organs (Palau and Espinós Orphanet J Rare Dis 1:47, 2006). ARCAs involve a wide range of clinical features including gait imbalance, diminished tendon reflexes, involuntary movements, and ophthalmological and cutaneous abnormalities. ARCAs are distinguished from other cerebellar ataxias by an autosomal recessive inheritance, onset before the age of 20 years, and slow progression (Fogel and Perlman Lancet Neurol 6:245-257, 2007).
Amyotrophic lateral sclerosis type 4 (ALS4, OMIM 602433) is a neurological disease characterized by juvenile onset, usually before the age of 25 years, a slow progression, and a normal life span. Typical symptoms include distal muscle weakness and atrophy, brisk deep-tendon reflexes, and a positive Babinski sign (Chen et al. Am J Hum Genet 74:1128-1135, 2004).
Genetics
Variants in the SETX gene cause one form of ARCAs: spinocerebellar ataxia, autosomal recessive 1 (SCAR1, OMIM 606002). Because oculomotor apraxia was observed in the initial patients with SETX variants, this form of the disease was also referred to as ataxia-oculomotor apraxia 2 (Moreira et al. Nat Genet 36:225-227, 2004). Subsequent reports detected oculomotor apraxia in only 50% of patients with SETX variants (Moreira and Koenig, GeneReveiws, 2007). SCAR1 patients constitute a heterogeneous group presenting with cerebellar ataxia and a range of additional features, including oculomotor apraxia, elevated serum levels of α-fetoprotein and creatine kinase (Moreira et al. Nat Genet 36:225-227, 2004), distal amyotrophy, peripheral neuropathy (Duquette et al. Ann Neurol 57:408-414, 2005; Asaka et al. Neurology 66:1580-1581, 2006) and nystagmus, spasticity and areflexia (Nicolaou et al. BMC Med Genet 9:28, 2008). At least 27 SETX variants have been reported in patients with SCAR1. These variants are distributed throughout the gene and include missense, nonsense, splicing and small deletions/insertions.
In addition to the SCAR1-causative variants, three dominant missense variants in the SETX gene were identified in patients with ALS4 (Chen et al. Am J Hum Genet 74:1128-1135, 2004), and one dominant missense variant was found in a Chinese patient with apparently isolated ALS (Zhao et al. Amyotroph Lateral Scler 10:118-122, 2009).
Clinical Sensitivity - Sequencing with CNV PG-Select
Currently unknown.
Testing Strategy
This test provides full coverage of all coding exons of the SETX gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Patients with SCAR1 (OMIM 606002) and patients with ALS 4 (OMIM 602433). This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SETX.
Patients with SCAR1 (OMIM 606002) and patients with ALS 4 (OMIM 602433). This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SETX.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| SETX | 608465 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Diseases
| Name | Inheritance | OMIM ID |
|---|---|---|
| Amyotrophic Lateral Sclerosis Type 4 | AD | 602433 |
| Spinocerebellar Ataxia Autosomal Recessive 1 | AR | 606002 |
Related Tests
| Name |
|---|
| Ataxia with Oculomotor Apraxia Panel |
| Distal Hereditary Motor Neuropathy Panel |
Citations
- Asaka, T., et.al. (2006). "Autosomal recessive ataxia with peripheral neuropathy and elevated AFP: novel mutations in SETX." Neurology 66(10): 1580-1. PubMed ID: 16717225
- Chen, Y. Z., et.al. (2004). "DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4)." Am J Hum Genet 74(6): 1128-35. PubMed ID: 15106121
- Duquette, A., et.al. (2005). "Mutations in senataxin responsible for Quebec cluster of ataxia with neuropathy." Ann Neurol 57(3): 408-14. PubMed ID: 15732101
- Fogel, B. L., Perlman, S. (2007). "Clinical features and molecular genetics of autosomal recessive cerebellar ataxias." Lancet Neurol 6(3): 245-57. PubMed ID: 17303531
- Maria-Céu Moreira, Michel Koenig (2009). "Ataxia with Oculomotor Apraxia Type 2." GeneReviews. PubMed ID: 20301333
- Moreira M.C. et al. 2004. Nature Genetics. 36: 225-7. PubMed ID: 14770181
- Nicolaou, P., et.al. (2008). "A novel c.5308_5311delGAGA mutation in Senataxin in a Cypriot family with an autosomal recessive cerebellar ataxia." BMC Med Genet 9: 28. PubMed ID: 18405395
- Palau, F., Espinos, C. (2006). "Autosomal recessive cerebellar ataxias." Orphanet J Rare Dis 1: 47. PubMed ID: 17112370
- Zhao, Z. H., et.al. (2009). "A novel mutation in the senataxin gene identified in a Chinese patient with sporadic amyotrophic lateral sclerosis." Amyotroph Lateral Scler 10(2): 118-22. PubMed ID: 19058054
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
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