In silico and structure-based assessment to classify VUS identified in the α-helical domain of BRCA2

Abstract

Breast cancer type 2 susceptibility (BRCA2) protein plays a crucial role in DNA double-strand breaks repair mechanism by homologous recombination. Pathogenic mutations in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer (HBOC). Different missense mutations are identified from a larger cohort of patient populations in the BRCA2. However, most missense mutations are classified as ‘Variants of Uncertain Significance’ (VUS) due to a lack of data from structural, functional, and clinical assessments. Therefore, this study focused on assessing VUS identified in the α-helical domain of h-BRCA2 using different in silico tools and structure-based molecular dynamics simulation. A total of 286 identified VUS were evaluated using Align-GVGD, PROVEAN and PANTHER servers and 18 variants were predicted to be pathogenic. Further, out of 18 variants analyzed using the ConSurf server, 16 variants were found to be evolutionary conserved. These 16 conserved variants were submitted to PremPS and Dynamut server to assess the effect of the mutation at the protein structure level; 12 mutations were predicted to have a destabilizing effect on the native protein structure. Finally, molecular dynamics simulations revealed 5 variants BRCA2 Cys2646Tyr, Asp2665Val, Trp2619Arg, Trp2619Ser and Tyr2660Cys can alter the folding pattern and need further validation using in vitro, structural and in vivo studies to classify as pathogenic.

Communicated by Ramaswamy H. Sarma

Keywords:

• BRCA2
• α-helical domain
• VUS
• molecular dynamics simulation
• PCA

Acknowledgement

The authors would like to thank the Bioinformatics Centre (BIC) at ACTREC for providing the necessary computational facility.

Disclosure statement

Authors show no conflict of interest.

Authors’ contributions

MAK, AKV designed the experiments; MAK performed the experiments; and MAK, AKV wrote the manuscript.

Additional information

Funding

This study was supported by the Department of Biotechnology, Ministry of Science and Technology (BT/PR40181/BTIS/137/15/2021) to AKV.