An overview of actionable and potentially actionable TSC1 and TSC2 germline variants in an online Database

Abstract

Tuberous Sclerosis Complex (TSC) is caused by loss of function germline variants in the TSC1 or TSC2 tumor suppressor genes. Genetic testing for the detection of pathogenic variants in either TSC1 or TSC2 was implemented as a diagnostic criterion for TSC. However, TSC molecular diagnosis can be challenging due to the absence of variant hotspots and the high number of variants described. This review aimed to perform an overview of TSC1/2 variants submitted in the ClinVar database. Variants of uncertain significance (VUS), missense and single nucleotide variants were the most frequent in clinical significance (37-40%), molecular consequence (37%-39%) and variation type (82%-83%) categories in ClinVar in TSC1 and TSC2 variants, respectively. Frameshift and nonsense VUS have potential for pathogenic reclassification if further functional and segregation studies were performed. Indeed, there were few functional assays deposited in the database and literature. In addition, we did not observe hotspots for variation and many variants presented conflicting submissions regarding clinical significance. This study underscored the importance of disseminating molecular diagnostic results in a public database to render the information largely accessible and promote accurate diagnosis. We encourage the performance of functional studies evaluating the pathogenicity of TSC1/2 variants.

Figure 1 -. Sunburst charts representing all variants with clinical significance and molecular consequence reported in the ClinVar Database. A) TSC1 variants distribution B) TSC2 variants distribution. The external layer represents the variant type and the internal layer represents the clinical significance. Percentages in the internal layer are represented in relation to the total variants. Percentages in the external layer are represented in relation to clinical significance.

Figure 2 -. Gene distribution of TSC1 single nucleotide variants (SNV) for benign or likely benign variants (B/LB), variants of uncertain significance (VUS), and pathogenic or likely pathogenic variants (P/LP). Intronic variants are not represented. Darker green dots represent missense variants. Yellow dots represent splice site variants. Black dots represent truncated variants (nonsense or frameshift deletions). Pink dots represent other variant types (synonymous, UTR and intronic variants). The TSC1 gene region that codes for TMD (predicted) and coiled coil domains are represented. The post translational modifications (PTM) are shown below the graphics (lighter green represents phosphorylation sites).

Figure 3 -. Gene distribution of TSC2 single nucleotide variants (SNV) for benign or likely benign variants (B/LB), variants of uncertain significance (VUS), and pathogenic or likely pathogenic variants (P/LP). Intronic variants are not represented. Darker green dots represent missense variants. Yellow dots represent splice site variants. Black dots represent truncated variants (nonsense or frameshift deletions). Pink dots represent other variant types (synonymous, UTR and intronic variants). The TSC2 gene regions that code for the Hamartin interaction region and GAP domain are demonstrated. The post translational modifications (PTM) are shown below the graphics (lighter green represents phosphorylation sites).

Figure 4 -. An overview of TSC1 and TSC2 VUS, conflicting and pathogenic variants submitted in ClinVar. A,B) Distribution of VUS with molecular consequence similar to pathogenic variants: frameshift, nonsense, splice site in TSC1 and TSC2, respectively. C) TSC1 and TSC2 B/LB vs VUS conflicting variants were separated in four groups: VUS>B/LB, B/LB>VUS, B/LB > VUS > B/LB, VUS > B/LB > VUS; D) TSC2 P/LP vs VUS conflicting variants were separated in four groups: VUS>P/LP, P/LP>VUS, P/LP > VUS > P/LP, VUS > P/LP > VUS; E) Representation of the time (in years) between a VUS submission and its reclassification as B/LB. F) Review status of TSC1 and TSC2 pathogenic variants; G) Number of submissions per TSC1 and TSC2 pathogenic variants in ClinVar; H) Year of the most recent submission of TSC1 and TSC2 pathogenic variants; I) Number of citations of TSC1 and TSC2 pathogenic variants.