Tuberous Sclerosis Complex via the TSC2 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 | |
|---|---|---|---|---|---|
| 3039 | TSC2 | 81407 | 81407,81406 | $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
Tuberous sclerosis complex (TSC1, OMIM 191100; TSC2, OMIM 613254) affects multiple organ systems including the skin (hypomelanotic macules, facial angiofibromas, shagreen patches, fibrous facial plaques, ungual fibromas); brain (e.g. cortical tubers, astrocytomas, seizures, intellectual disability/developmental delay); kidney (cysts, renal cell carcinomas); heart (rhabdomyomas, arrhythmias); and lungs (lymphangioleiomyomatosis [LAM]) (Northrup et al. 2020. PubMed ID: 20301399). It affects nearly 1 in 5800 children in the United States (Osborne et al. Ann N Y Acad Sci. 615:125, 1991).
Genetics
Tuberous sclerosis complex (TSC) is mainly caused by variants in the TSC1 and TSC2 genes, which are tumor suppressors that are involved in cellular proliferation and act thorough multiple signaling pathways (e.g. mTOR/AKT pathways) (Orlova et al. Ann N Y Acad Sci 1184:87, 2010). TSC is inherited in an autosomal dominant manner with two-thirds of cases resulting from sporadic germline variants and one-third of cases inherited from an affected parent. It presents with complete penetrance but with variable expressivity. Phenotypes of TSC types can be similar, but TSC2 variants are reported to cause a more severe clinical presentation (Northrup et al. 2020. PubMed ID: 20301399). Truncating variants are found in the majority of TSC cases, and variants reported to date include missense, splice site, small insertions and deletions, and large deletions (Human Gene Mutation Database).
Clinical Sensitivity - Sequencing with CNV PG-Select
Variants can be identified in approximately 95% of individuals with tuberous sclerosis; 5% of individuals with TSC will not have a variant identified. Variants identified in TSC2 are found in 69% of patients (Northrup et al. 2020. PubMed ID: 20301399). Deletions and duplications are found in up to 2% of TSC2 variants (Northrup et al. 2020. PubMed ID: 20301399). TSC shows a high degree of somatic mosaicism, and sequence change levels that are less than 10% may be difficult to detect via sequencing.
Testing Strategy
This test provides full coverage of all coding exons of the TSC2 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Individuals with a clinical presentation of tuberous sclerosis or having a family history of tuberous sclerosis. Earlier detection of clinical abnormalities can lead to earlier treatment and better outcomes. This test is specifically designed for heritable germline variants and is not appropriate for the detection of somatic variants in tumor tissue.
Individuals with a clinical presentation of tuberous sclerosis or having a family history of tuberous sclerosis. Earlier detection of clinical abnormalities can lead to earlier treatment and better outcomes. This test is specifically designed for heritable germline variants and is not appropriate for the detection of somatic variants in tumor tissue.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| TSC2 | 191092 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Tuberous Sclerosis 2 | AD | 613254 |
Related Tests
Citations
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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