1. NGS panel - Genetic testing for tuberous sclerosis

Tuberous sclerosis

May 30, 2017

Clinical features

Tuberous sclerosis complex is a genetic disorder characterized by the growth of numerous benign tumors in different body parts, including skin, brain, kidneys, and other organs.

Tuberous sclerosis complex (TSC) should be suspected in individuals with some of the following major and/or minor clinical features of the disease:

The major clinical features of tuberous sclerosis are:

  • Hypomelanotic macules
  • Facial or other angiofibromas
  • Shagreen patches
  • Ungual fibromas
  • Cortical dysplasias, including tubers and cerebral white matter migration lines
  • Cardiac rhabdomyoma
  • Lymphangioleiomyomatosis
  • Multiple retinal nodular hamartomas
  • Renal angiomyolipoma
  • Subependymal giant cell astrocytoma
  • Subependymal nodules.

Minor clinical features of tuberous sclerosis are:

  • “Confetti“ skin lesions (hypopigmented macules scattered over regions of the body
  • Dental enamel pits
  • Retinal achromic patch
  • Intraoral fibromas
  • Nonrenal hamartomas or multiple renal cysts.

The diagnosis of TSC is based on clinical findings, but genetic background of the disease is also very common. Thus, heterozygous pathogenic variants can be identified in 75-90% of individuals who meet the clinical diagnostic criteria for TSC 1. Among those in whom a pathogenic variant can be identified, TSC1 pathogenic variants are found in 24% and TSC2 pathogenic variants in 66% 1, 2, 5, 6. Pathogenic variants have been identified so far in more than 4200 individuals with TSC and their families. Tuberous sclerosis is generally caused by mutations in one of the two genes seen as responsible: TSC1 and TSC2.

Hamartin (encoded by TSC1) and tuberin (encoded by TSC2) function as a complex which controlls cell growth and division, via interactions with the mTOR pathway 4. Mutations in TSC1 and TSC2 result in a loss of control of cell growth and division, and thus patients develop a high predisposition to form different tumors. TSC affects tissues from different germ layers, creating cutaneous and visceral tumors, adenoma sebaceum, cardiac rhabdomyomas, renal angiomyolipomas and renal cancers in general 1, 4. Brain lesions seen in patients with tuberous sclerosis include hamartomas of the cortex, ventricular walls, and subependymal giant cell tumors.

The overall incidence of TSC is estimated to be as high as 1:5,800 live births 7. A high mutation rate is also suggested and is estimated at 1:250,000 per gene per generation 8.

TSC1 encodes the protein harmatin, essential for protein-protein interactions within the cytoskeleton. A major function of hamartin is to stabilize the hamartin-tuberin complex and facilitate the GTPase-activating function of tuberin in the complex. Harmatin also regulates growth of neurites, and synapse formation, as well as axon development. Almost all TSC1 pathogenic variants are predicted to cause truncation of the hamartin protein; and more than 500 unique TSC1 pathogenic variants have been identified in thousands of individuals/families worldwide 2, 5. Most pathogenic variants are unique but a few are known to recur, including those in specific codons of exon 15. Other pathogenic variants are scattered throughout the exons and splice sites.

The TSC2 gene encodes protein tubulin, closely associated with hamartin mentioned above. More than 1,400 unique TSC2 pathogenic variants have been identified in over 3600 affected individuals/families and approximately 33% 1, 2, 3 of TSC2 pathogenic variants are located in exons 32-41 2, 3, 5 which encode the carboxy domain of tuberin consisting of several important functional motifs, such as calcium/calmodulin binding domains, GAP domain, estrogen receptor, and multiple signal pathway kinase targets. Missense variants account for approximately 29% 2, 3, 5 of all TSC2 pathogenic variants with approximately 50% of mutations concentrated in the carboxy domain 1.

There is no cure for tuberous sclerosis and so far symptomatic therapy is the best possible choice, including mTOR inhibitors, vigabatrin and other antiepileptic drugs for the seizures, and neurosurgery in cases of life-threatening neurological symptoms. Clinical trials are in progress with possible new drugs, such as Everolimus, Infliximab, Nilotibin, and others.

CENTOGENE offers the Tuberous sclerosis panel, including full gene sequencing (genes: TSC1, TSC2) and deletion/duplication analysis of both panel genes. In addition, any of the genes in the Tuberous sclerosis panel can also be ordered individually, for full gene sequencing and deletion/duplication analysis.


The majority of pathogenic variants in the ADAR gene result in autosomal recessive disease. Missense, nonsense, frameshift, and splice site pathogenic variants have been reported. One missense variant, p.Pro193Ala, is common in individuals of European origin 1, 3. One dominant variant, p.Gly1007Arg, has been reported 3, 4.

All IFIH1 pathogenic variants associated with AGS to date have been missense variants that cause dominant disease. IFIH1 encodes the interferon-induced helicase C domain-containing protein 1, a cytosolic double-stranded RNA receptor 1, 2.

The majority of pathogenic variants in RNASEH2A are missense; but splicing and frameshift pathogenic variants have also been reported 2, 3.

The frequency of some RNASEH2B alleles identified in affected individuals is determined 3:

  • p.Ala177Thr (62%)3
  • p.Thr163Ile (7%)3
  • p.Val185Gly (7%)3
  • c.136+1delG (4%)3.

All pathogenic variants identified in RNASEH2C so far are missense 5 and one of the RNASEH2C alleles has the highest frequency: ~72% for p.Arg69Trp 2, 3.

The majority of pathogenic variants in the SAMHD1 gene are missense, splice site, nonsense, or frameshift variants 6. A recurrent deletion including exon 1 has been observed in several affected individuals of Ashkenazi Jewish ancestry and it is considered a founder variant 7. Furthermore, a recurrent splice acceptor site pathogenic variant (c.1411-2A>G) in intron 12 is seen in persons of Amish ancestry and represents an ancient founder variant 8.

All pathogenic variants associated with TREX1-related AGS were detectable by sequence analysis. A recurrent p.Arg164Ter founder variant in TREX1 is seen in individuals of Cree ancestry 9. The most prevalent TREX1 variant in AGS is a missense change (p.Arg114His) that is particularly common in people from northern Europe 1, 2, 5.

Treatment of manifestations for AGS mainly includes treatment of respiratory complications as well as chest physiotherapy. Special diet and feeding methods are used to assure adequate caloric intake and avoid aspiration; management of seizures is performed using standard protocols. Clinical trials are in progress with new possible drugs being tested for AGS treatment (for example: Reverse transcriptase inhibitors: Zidovudine, Lamivudine, Abacavir).

CENTOGENE offers the Aicardi-Goutieres syndrome panel, including full gene sequencing (genes: ADAR, IFIH1, TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1) and deletion/duplication analysis of selected genes (RNASEH2B, RNASEH2A, TREX1, RNASEH2C, and SAMHD1). In addition, any of the genes in the Aicardi-Goutieres syndrome panel can also be ordered individually, for full gene sequencing and deletion/duplication analysis.


Differential diagnosis

The differential diagnosis of tuberous sclerosis-related disorders – depending on the major symptoms in the initial case – includes the following diseases:

  • Skin manifestations

    • Hypopigmented macules (observed in 0.8% of newborns 9)
    • Angiofibromas, frequently mistaken for acne vulgaris, acne rosacea, or multiple trichoepithelioma
    • Connective tissue nevus, the term that includes a variety of skin lesions with excessive dermal connective tissue that are not necessarily associated with TSC
    • Ungual fibromas resulting from trauma

  • Kidneys

    • Renal cysts
    • Renal angiomyolipomas (AMLs)

  • Lungs

    • Lymphangioleiomyomatosis (LAM) observed in female patients who also have renal angiomyolipomas but no other findings of TSC

  • Heart

    • Cardiac rhabdomyomas


Testing strategy

CENTOGENE offers advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on the PCR-free Whole Genome Sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and provides sequencing of entire gene at a more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for tuberous sclerosis using NGS Panel Genomic targeted towards this specific phenotype:

Step 1: Whole genome sequencing from a single filter card. The sequencing covers the entire genic region (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the Tuberous sclerosis panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the Tuberous sclerosis panel, based on the approval and consent, we further recommend to continue the bioinformatics analysis of the data obtained by whole genome sequencing to cover genes that are either implicated in an overlapping phenotype or could be involved in a similar pathway but not strongly clinically implicated based on the current information in literature.


Referral reasons

The following individuals are candidates for tuberous sclerosis gene testing:

  • Individuals with a family history of tuberous sclerosis and presentation of the most common symptoms, including hypomelanotic macules, facial angiofibromas, shagreen patches, cortical dysplasias, subependymal nodules, seizures, kidney cysts, rhabdomyomas and others
  • Individuals without a positive family history, but with symptoms resembling tuberous sclerosis
  • Individuals with a negative but suspected family history, in order to perform proper genetic counseling (prenatal analyses are recommended in families with affected individuals).

Test utility

Sequencing, deletion/duplication of the TSC1 and TSC2 genes should be performed in all individuals suspected for tuberous sclerosis. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of mutations, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis of tuberous sclerosis through genetic testing can allow for genetic counseling and may direct medical management.

Genetic counseling can provide a patient and/or family with the natural history of tuberous sclerosis, to identify at-risk family members, provide reproductive risks as well as possible preventive therapy or preconception/prenatal options, and allow for appropriate referral for patient support and/or resources.


More information on CENTOGENE´s Tuberous sclerosis panel can be found in our genetic test catalogue.