Spastic Paraplegia 49 via the TECPR2 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 | |
|---|---|---|---|---|---|
| 5039 | TECPR2 | 81479 | 81479,81479 | $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
Spastic paraplegia 49 (SPG49) is a type of hereditary spastic paraplegia (HSP) (Lo Giudice et al. 2014). SPG49 has been described in Jewish Bukharian families with early onset of spastic paraplegia, mental retardation, delayed psychomotor development and thin corpus callosum on brain imaging. Some affected individuals may also have dysmorphic features, e.g., short stature, short broad neck, low anterior hairline, round face, dental crowding and chubby appearance (Oz-Levi et al. 2012; Zhu et al. 2015). In addition to evolving spasticity and intellectual disability, patients from non-Bukharian families reported by Heimer et al. (2016) also manifest autonomic-sensory neuropathy accompanied by chronic respiratory disease.
Genetics
The transmission manner in the reported families with SPG49 is consistent with autosomal recessive (AR) inheritance (Oz-Levi et al. 2012; Zhu et al. 2015; Heimer et al. 2016). Pathogenic variants in TECPR2 (tectonin beta-propeller repeat containing 2) gene are causative for this form of complex spastic paraplegia. The TECPR2 protein belongs to the tectonin β-propeller repeat-containing protein family, containing WD (tryptophan-aspartic acid repeat) and TECPR domains (Oz-Levi et al. 2013). Functional studies using skin fibroblasts from SPG49 patients show that the TECPR2 protein has a positive role in autophagy. Pathogenic variants in TECPR2 gene may induce accumulation of dysfunctional proteins in neurons leading them to death (Oz-Levi et al. 2013; Behrends et al. 2010). Reported TECPR2 pathogenic variants include missense and small frameshift deletions (Human Gene Mutation Database).
Clinical Sensitivity - Sequencing with CNV PG-Select
It is difficult to estimate the clinical sensitivity of this test due to the lack of large cohort studies. All reported pathogenic variants to date in TECPR2 gene are detectable by sequencing.
Testing Strategy
This test provides full coverage of all coding exons of the TECPR2 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Patients showing features consistent with AR-HSP, intellectual disability, and autonomic-sensory neuropathy are candidates for this test. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TECPR2.
Patients showing features consistent with AR-HSP, intellectual disability, and autonomic-sensory neuropathy are candidates for this test. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TECPR2.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| TECPR2 | 615000 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Spastic Paraplegia 49 | AR | 615031 |
Citations
- Behrends C. et al. 2010. Nature. 466: 68-76. PubMed ID: 20562859
- Heimer G. et al. 2016. European Journal of Paediatric Neurology. 20: 69-79. PubMed ID: 26542466
- Human Gene Mutation Database (Bio-base).
- Lo Giudice T. et al. 2014. Experimental Neurology. 261: 518-39. PubMed ID: 24954637
- Oz-Levi D. et al. 2012. American Journal of Human Genetics. 91: 1065-72. PubMed ID: 23176824
- Oz-Levi D. et al. 2013. Autophagy. 9: 801-2. PubMed ID: 23439247
- Zhu X. et al. 2015. Genetics in Medicine. 17: 774-81. PubMed ID: 25590979
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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ORDER OPTIONS
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2) Select Additional Test Options
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