Novel Frameshift Deletion Pathogenic Variant Characterization in Tuberous Sclerosis-2 Using Exome Sequencing and...

Area of Science:

• Genetics
• Biochemistry
• Computational Biology

Background:

• Tuberous sclerosis complex (TSC) is a rare genetic disorder caused by mutations in TSC1 or TSC2 genes.
• Mutations in TSC2 are associated with more severe symptoms and earlier onset.
• Accurate genetic diagnosis is crucial for understanding disease mechanisms and patient management.

Purpose of the Study:

• To identify and characterize a novel pathogenic variant in the TSC2 gene.
• To investigate the structural and functional consequences of the identified variant using computational methods.
• To evaluate the utility of exome sequencing in diagnosing TSC and informing genetic counseling.

Main Methods:

• Exome sequencing (ES) was employed to detect the causative variant.
• Sanger sequencing and cosegregation analysis confirmed the variant.
• GROMACS software was used for molecular dynamics (MD) simulations to assess the variant's impact on tuberin protein structure and function.
• Variant interpretation followed the American College of Medical Genetics and Genomics (ACMG) guidelines.

Main Results:

• A novel de novo frameshift deletion variant (c.3647_3651del, p.Leu1216Profs*16) was identified in the TSC2 gene of a 12-year-old male patient with TSC symptoms.
• The mutation, located in exon 31, meets ACMG criteria for pathogenicity.
• MD simulations revealed that the mutation disrupts the GAP domain, breaks hydrogen bonds, reduces solvent exposure, and alters tuberin's stability and conformational dynamics.

Conclusions:

• Exome sequencing is an effective tool for TSC diagnosis and genetic counseling.
• Computational analysis provides valuable molecular insights into TSC pathogenesis.
• The identified TSC2 variant's effects suggest potential therapeutic strategies targeting the mTOR pathway, such as using mTOR inhibitors.