Tuberous sclerosis: catching mosaicism and intronic mutations

Recommended testing at Breda Genetics for this condition (also to test for mosaicism):

Tuberous sclerosis (TSC1, TSC2)

If negative: MLPA analysis (TSC1, TSC2 gene).

If negative: Exonic ultra-deep sequencing (600x) and SNaPshot analysis

Mosaicism in TSC1 & TSC2: CT scanSummary

Tuberous Sclerosis Complex (TSC), also called Bourneville syndrome, is a multisystem disorder with variable expressivity characterized by hamartomas in multiple organ systems. It mainly affects the brain and the skin, with possible manifestations in kidneys, heart and lungs.

Brain manifestations: Cortico/subcortical tubers and subependymal nodules are typical and occur in most patients. Early-onset epilepsy (infantile spasms and/or focal seizures) is also very frequent, appearing in approximately 85% of cases. Subependymal giant cell astrocytomas (SEGAs) can be found in about 15% of patients. Intellectual disability is a typical feature of TSC and frequently occurs alongside with other neurological manifestations like attention-deficit/hyperactivity and autism spectrum disorders, self-injury, anxiety and obsessive compulsive tendencies. Due to high inter and intra-familial variability, however, some patients may have minimal symptoms with no neurologic disability. Tumors of the central nervous system are the leading cause of morbidity and mortality.

Skin manifestations: hypomelanotic macules (very frequent), facial angiofibromas, shagreen patches, fibrous cephalic plaques and ungual fibromas. Skin lesions do not usually represent a serious medical problem.

Other abnormalities: Renal angiomyolipomas, cysts, renal cell carcinomas (renal disease is the second leading cause of early death), cardiac rhabdomyomas and arrhythmias, lymphangioleiomyomatosis in the lungs, dental enamel pitting, intraoral fibromas and skeletal dysplasias.

The diagnosis of TSC can be either clinical (according to definite criteria) or genetic.

Mutational spectrum and testing methods

The TSC1 and TSC2 genes are located on the chromosomal regions 9q34.13 and 16p13.3Mosaicism in tuberous sclerosis
respectively. The TSC1 gene encodes hamartin, a protein that interacts with tuberin (encoded by TSC2) to form a complex which is key in the regulation of cell growth, cell survival and cell cycle progression. Heterozygous pathogenic variants in TSC1 (31%) or TSC2 (69%) can be identified in about 85% of individuals affected by TSC. Approximately 15% of persons with tuberous sclerosis have no mutation at sequencing or MLPA. More than harbouring a mutation in a third unknown gene (which is nowadays considered unlikely), these persons most probably have somatic mosaicism for a TSC1 or TSC2 mutation which cannot be detected by the standard techniques. DNA testing of other tissues (tumor tissue in particular, but also saliva, skin and/or hair follicles) is warranted when somatic mosaicism is suspected and routine molecular genetic testing on peripheral blood has not revealed a mutation. Alternatively, exonic ultra deep sequencing (of peripheral blood or other tissues) may be used.

Most mutations are protein truncating and are consistent with small deletions and insertions of few nucleotides or nonsense mutations. Splice mutations (which can also be deeply located in the intron at hundreds of base pairs from the exon/intron junctions) are very frequent too. Large deletions/duplications identifiable by MLPA are estimated to have a frequency of 5%. Missense mutations are the rarest (4,1%). The majority of mutations are unique, but a bunch of common, recurring mutations is also known (e.g. in exon 15).

Testing Method: TSC1 and TSC2 genes: full sequencing of the entire gene loci (all exons, all introns and 5′-3’UTRs – NGS). Alternatively: sequencing of the coding regions plus large intronic tracts from the exon/intron boundaries and part of the 5’UTR (NGS, Sanger). If negative: MLPA analysis for TSC2 and TSC1. If negative: sequencing and MLPA on DNA from other tissues (tumor tissue in particular, but also saliva, skin and/or hair follicles) or exonic ultra-deep sequencing (NGS, coverage 600x) with subsequent allele-specific PCR and/or SNaPshot analysis to both confirm and quantify the proportion of the mosaic mutation.

The penetrance of TSC has been estimated to be nearly 100%, therefore, when the mutation has been inherited, the parent is usually symptomatic or paucisymptomatic. However, at least two thirds of TSC patients have the disease as the result of a de novo mutation and the parents are therefore not affected.

Genotype-phenotype correlations: TSC2 mutations are associated with more severe disease, showing a higher frequency of intellectual disability, autistic disorder, low IQ, infantile spasms and a greater risk for renal malignancy. A contiguous gene deletion syndrome causing the loss of both TSC2 and the adjacent PKD1 gene has been found in more than one case. In these patients the phenotype is mixed and become evident in utero or early in infancy.

Differential Diagnosis

Many tuberous sclerosis features are nonspecific and can be seen as isolated findings or as manifestation of other diseases. Interestingly, a single facial angiofibroma is not diagnostic of tuberous sclerosis. and the shagreen patch of tuberous sclerosis does not differ from other connective tissue nevi and hypopigmented macules which, in most cases, have no medical significance.

Recommended testing at Breda Genetics for this condition:

Tuberous sclerosis (TSC1, TSC2)

If negative: MLPA analysis (TSC1, TSC2 gene).

If negative: Exonic ultra-deep sequencing (600x) and SNaPshot analysis


Tuberous Sclerosis Complex. Northrup H, Koenig MK, Pearson DA, Au KS. In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Stephens K, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2018. 1999 Jul 13 [updated 2018 Jul 12]. PMID:20301399

Mosaic and Intronic Mutations in TSC1/TSC2 Explain the Majority of TSC Patients with No Mutation Identified by Conventional Testing. Tyburczy ME, Dies KA, Glass J, Camposano S, Chekaluk Y, Thorner AR, Lin L, Krueger D, Franz DN, Thiele EA, Sahin M, Kwiatkowski DJ.PLoS Genet. 2015 Nov 5;11(11):e1005637. PMID:26540169,

Targeted Next Generation Sequencing reveals previously unidentified TSC1 and TSC2 mutations. Nellist M, Brouwer RW, Kockx CE, van Veghel-Plandsoen M, Withagen-Hermans C, Prins-Bakker L, Hoogeveen-Westerveld M, Mrsic A, van den Berg MM, Koopmans AE, de Wit MC, Jansen FE, Maat-Kievit AJ, van den Ouweland A, Halley D, de Klein A, van IJcken WF. BMC Med Genet. 2015 Feb 25;16:10. PMID:25927202

Ultra deep sequencing detects a low rate of mosaic mutations in tuberous sclerosis complex. Qin W1, Kozlowski P, Taillon BE, Bouffard P, Holmes AJ, Janne P, Camposano S, Thiele E, Franz D, Kwiatkowski DJ. Hum Genet. 2010 Mar;127(5):573-82. doi: 10.1007/s00439-010-0801-z. Epub 2010 Feb 18. PMID:20165957

OMIM: 191100, 605284, 191092, 613254, 601231.

Orphanet: ORPHA805.

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