First comprehensive TSC1/TSC2 mutational analysis in Mexican patients with Tuberous Sclerosis Complex reveals numerous novel pathogenic variants

Miriam E Reyna-Fabián,Nancy L Hernández-Martínez,Carlos G Todd-Quiñones,José A Velázquez-Aragón,Ariadna González-Del Angel,Alfredo Varela-Echavarría,Sergio Enríquez-Flores,Miguel A Alcántara-Ortigoza,Jorge T Ayala-Sumuano

doi:10.1038/s41598-020-62759-5

Abstract

The aim of this study was to improve knowledge of the mutational spectrum causing tuberous sclerosis complex (TSC) in a sample of Mexican patients, given the limited information available regarding this disease in Mexico and Latin America. Four different molecular techniques were implemented to identify from single nucleotide variants to large rearrangements in the TSC1 and TSC2 genes of 66 unrelated Mexican-descent patients that clinically fulfilled the criteria for a definitive TSC diagnosis. The mutation detection rate was 94%, TSC2 pathogenic variants (PV) prevailed over TSC1 PV (77% vs. 23%) and a recurrent mutation site (hotspot) was observed in TSC1 exon 15. Interestingly, 40% of the identified mutations had not been previously reported. The wide range of novels PV made it difficult to establish any genotype-phenotype correlation, but most of the PV conditioned neurological involvement (intellectual disability and epilepsy). Our 3D protein modeling of two variants classified as likely pathogenic demonstrated that they could alter the structure and function of the hamartin (TSC1) or tuberin (TSC2) proteins. Molecular analyses of parents and first-degree affected family members of the index cases enabled us to distinguish familial (18%) from sporadic (82%) cases and to identify one case of apparent gonadal mosaicism.

Highlights

Tuberous sclerosis complex (TSC; MIM #191100, MIM #613254) is an autosomal dominant syndrome characterized by the presence of multiple hamartomas in different organs and systems
A customized bioinformatic analysis enabled us to identify a pathogenic variants (PV) in 10 cases; we found one case (ET243) with a missense variant p.(Trp1060Ser) in TSC2 that was classified as an LPV20 and one case (ET81) with an intronic variant c.3815–21G>A in TSC1 that was classified [PP3, PP4]20 as a variant of uncertain significance or VUS (Tables 1,2)
Most of the 62 PV/likely pathogenic variants (LPV) were present in TSC2 (77% compared to 23% in TSC1) and there was a greater proportion of small variants (SV) (90%) compared to copy number variants (CNV) (10%)

Summary

Introduction

Tuberous sclerosis complex (TSC; MIM #191100, MIM #613254) is an autosomal dominant syndrome characterized by the presence of multiple hamartomas in different organs and systems. TSC is caused by pathogenic variants (PV) in the tumor suppressor-genes, TSC1 (tuberous sclerosis complex 1, MIM *605284, 9q34.13) and TSC2 (tuberous sclerosis complex 2, MIM *191092, 16p13.3). These PV can be detected by various molecular techniques, such as single-strand conformational polymorphism (SSCP), direct Sanger sequencing (SS), multiplex ligation-dependent probe amplification (MLPA) and next-generation sequencing (NGS). In order to improve our knowledge of this disease and to spread the use of innovative and highly sensitive molecular techniques such as MLPA and NGS for the diagnosis of TSC in countries where the disease has been under-studied, we used a combined molecular strategy to analyze the mutational spectrum of TSC1 and TSC2 and the principal clinical features of 66 Mexican-descent unrelated cases of TSC

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