Mutational analysis of TSC1 and TSC2 in Danish patients with tuberous sclerosis complex

Abstract

tuberous sclerosis complex (tSc) is an autosomal dominant disorder characterized by hamartomas in the skin and other organs, including brain, heart, lung, kidney and bones. tSc is caused by mutations in TSC1 and TSC2. Here, we present the TSC1 and TSC2 variants identified in 168 Danish individuals out of a cohort of 327 individuals suspected of TSC. A total of 137 predicted pathogenic or likely pathogenic variants were identified: 33 different TSC1 variants in 42 patients, and 104 different TSC2 variants in 126 patients. In 40 cases (24%), the identified predicted pathogenic variant had not been described previously. In total, 33 novel variants in TSC2 and 7 novel variants in TSC1 were identified. To assist in the classification of 11 TSC2 variants, we investigated the effects of these variants in an in vitro functional assay. Based on the functional results, as well as population and genetic data, we classified 8 variants as likely to be pathogenic and 3 as likely to be benign. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder of high penetrance with an incidence of 1:6,000-1:10,000 and an estimated prevalence of 1:14,000-1:25,000 1,2. TSC is characterized by the presence of mainly benign tumors that can affect multiple organ systems e.g. the central nervous system, heart, kidney, lung, bone and skin. TSC patients are phenotypically and genetically heterogeneous and there is considerable variation in the number, location and size of the different TSC-associated lesions. Mutations in one of two genes, TSC1 (OMIM#191100) and TSC2 (OMIM#191092), cause TSC 3,4. TSC1 is located on chromosome 9q34 and consists of 23 exons, which encode the 130 kDa TSC1 protein, hamartin. TSC2 is located on chromosome 16p13.3 and consists of 42 exons which encode the 200 kDa TSC2 protein, tuberin. TSC1 and TSC2, together with a third subunit, TBC1D7 5 , form a stable protein complex, the TSC complex. The TSC complex is a GTPase-activating protein (GAP) specific for the small GTPase, Ras homologue enriched in brain (RHEB) 6. Active RHEB is involved in the activation of the mechanistic target of rapamycin (mTOR) complex 1 (mTORC1), a critical regulator of anabolic processes such as protein and lipid synthesis 7. The TSC complex inactivates RHEB to down-regulate mTORC1 signaling and inhibit cell growth. TSC-associated tumors are characterized by increased phosphorylation of S6, elongation factor 4E binding protein 1 (4E-BP1), p70 S6 kinase (S6K) and other downstream targets of mTORC1 (Fig. 1). Approximately 2/3 of TSC cases are due to sporadic de novo germline mutations 2. TSC2 mutations are identified in the majority of TSC patients and, in general, cause a more severe phenotype than TSC1 mutations 8,9. Exceptions to this rule are however observed 10,11. Large genomic deletions that affect both TSC2 and the adjacent PKD1 (OMIM# 601313) locus are associated with a subset of patients with TSC and severe, early-onset autosomal dominant polycystic kidney disease. While a pathogenic TSC1 or TSC2 variant can be identified in m...

Renal phenotypes correlate with genotypes in unrelated individuals with tuberous sclerosis complex in China

“…Additionally, we found that 29% TSC1 variants were familial variants, whereas only 9% TSC2 variants were inherited from families, which is consistent with the results of the previous studies [ 15 , 21 , 22 ]. We confirmed the higher frequency of familial TSC1 variants compared to that of familial TSC2 variants, which is attributed to the smaller size and simpler structure of the TSC1 genomic locus, and the rarity of missense mutations, frames shift mutations and large rearrangements at the locus [ 12 ]. A large number of TSC1 variants was observed in familial cases probably because patients with TSC1 variants are less likely to be affected by severe neurocognitive impairment and are therefore more likely to have offspring [ 13 , 23 ].…”

“…In this study, we identified 161 variants in 173 unrelated patients (93%), including 27 (16%) with TSC1 variants and 134 (77%) with TSC2 variants, which is higher than that reported in other countries [ 12 – 15 ]. This is due to the NGS applied in this study.…”

The PI3K/mTOR Pathway Is Targeted by Rare Germline Variants in Patients with Both Melanoma and Renal Cell Carcinoma

“…Germline heterozygous mutations in TSC1 are known to be responsible for hamartoma syndromes, including tuberous sclerosis (TS) that confer increased susceptibility to renal cancer [ 64 ]. Of note, the TSC1 variants observed in our series were located in exons 17 and 18, encoding part of the tuberin-binding region regularly targeted in TS [ 65 ].…”

Non-Canonical Functions of a Mutant TSC2 Protein in Mitotic Division

“…This particular TSC2 mutation (c.5238_5255del, p. (His1746_Arg1751del of 6 amino acids in exon 41) has been frequently reported. In fact, in multiple studies profiling mutations in patients with TSC throughout the world, this same 6 amino acids deletion was found to be the most common mutation (Dabora et al ., 2001; Jones et al, 1999; Reyna-Fabián et al, 2020; Rosengren et al, 2020; Wang et al, 2013). The impact from this specific mutant microdeletion allele thus has important consequences for patients with TSC globally.…”