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Tuberous Sclerosis Complex (TSC) Deletion/Duplication Testing via MLPA

Summary and Pricing

Test Method

Multiplex Ligation-Dependent Probe Amplification Assay
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
TSC1 81405
TSC2 81406
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
2055Genes x (2)81479 81405(x1), 81406(x1) $540 Order Options and Pricing

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

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.


Genetic Counselors


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Tuberous Sclerosis Complex affects multiple organ systems including the skin (hypomelanotic macules, facial angiofibromas, shagreen patches, fibrous facial plaques, ungual fibromas), brain (cortical tubers, astrocytomas, seizures, intellectual disability/developmental delay), kidney (cysts, renal cell carcinomas), heart (rhabdomyomas, arrhythmias), and lungs (lymphangioleiomyomatosis [LAM]) (Northrup et al. 2018. PubMed ID: 20301399). It affects about 1 in 5,800 children in the United States (Osborne et al. 1991. PubMed ID: 2039137). Nearly 100% of individuals with TSC have skin or dental findings detectable via physical examination. Individuals who meet specific clinical findings (major and minor features) and/or have a pathogenic variant in one of the TSC genes have a definite diagnosis of Tuberous Sclerosis (Northrup and Krueger. 2013. PubMed ID: 24053982). For brain abnormalities, such as subependymal giant cell astrocytomas, either surgical resection or mTOR inhibitors can be utilized depending on the presence of singular or multiple lesions. Surveillance of brain, kidney, lung, teeth and other pertinent organs for disease progression have previously been recommended at specific intervals (1-3 years) to include periodic magnetic resonance imaging (MRI), computed tomography (CT), echocardiogram, electroencephalograph (EEG), dermatologic and eye exams (Krueger and Northrup. 2013. PubMed ID: 24053983).


Tuberous Sclerosis Complex (TSC) is caused by pathogenic variants in the TSC1 and TSC2 genes. These genes are tumor suppressors that are involved in cellular proliferation and act through multiple signaling pathways (mTOR/AKT pathways) (Orlova and Crino. 2010. PubMed ID: 20146692). TSC is inherited in an autosomal dominant manner with two-thirds of cases resulting from sporadic germline mutations while one-third of cases are inherited from an affected parent. It presents with near complete penetrance, but has variable expressivity. Phenotypes of TSC types can be similar, but TSC2 pathogenic variants are reported to cause a more severe clinical presentation (Northrup et al. 2018. PubMed ID: 20301399). Causative variants reported to date include nonsense, missense, splice site, small insertions and deletions, and large duplications and deletions (Human Gene Mutation Database). Truncating variants are found in the majority of TSC cases.

Clinical Sensitivity - MLPA

This test is only for deletion/duplication testing. For sequencing and deletion/duplication testing see test code 10661.

Individuals with an identifiable TSC pathogenic variant will have either a large deletion or duplication in up to 2% and 0.5% of cases in the TSC2 and TSC1 genes, respectively (Northrup et al. 2018. PubMed ID: 20301399).

Testing Strategy

Multiplex Ligation-Dependent Probe Amplification (MLPA) enables the detection of deletion and duplications of single and multiple exons within a given gene (Eijk-Van Os and Schouten. 2011). This test involves analysis only of the specific gene(s) of interest for each patient. The MLPA test is designed to have coverage for all exons for each targeted gene. It is a semi-quantitative technique to determine relative copy number using a multiplex PCR-based reaction. Only hybridized and ligated adjacent probe oligonucleotides of approximately 60 nucleotides in length are amplified using PCR and thus are specific for the sequence of interest. A stuffer sequence attached to the probe ensures a particular length for deciphering the probe target. Therefore, MLPA enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. For additional information please see www.mlpa.com.

Indications for Test

This test is only for deletion/duplication testing. For sequencing and deletion/duplication testing see test code 10661.

Individuals with a clinical presentation of tuberous sclerosis or having a family history of tuberous sclerosis who may have had negative sequencing results. Early diagnosis can lead to better outcomes. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.


Official Gene Symbol OMIM ID
TSC1 605284
TSC2 191092
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Tuberous Sclerosis 1 AD 191100
Tuberous Sclerosis 2 AD 613254

Related Tests

Interstitial Lung Disease Panel
Tuberous Sclerosis Complex via the TSC1 Gene
Tuberous Sclerosis Complex via the TSC2 Gene


  • Eijk-Van Os and Schouten. 2011. PubMed ID: 20938835
  • Human Gene Mutation Database (Bio-base).
  • Krueger and Northrup. 2018. PubMed ID: 24053983
  • Northrup and Krueger. 2013. PubMed ID: 24053982
  • Northrup et al. 2020. PubMed ID: 20301399
  • Orlova and Crino. 2010. PubMed ID: 20146692
  • Osborne et al. 1991. PubMed ID: 2039137


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

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2) Select Additional Test Options

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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