A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases

Sci Rep. 2021 Jul 12;11(1):14268. doi: 10.1038/s41598-021-93715-6.


DNA-Damage Response (DDR) proteins are crucial for maintaining the integrity of the genome by identifying and repairing errors in DNA. Variants affecting their function can have severe consequences since failure to repair damaged DNA can result in cells turning cancerous. Here, we compare germline and somatic variants in DDR genes, specifically looking at their locations in the corresponding three-dimensional (3D) structures, Pfam domains, and protein-protein interaction interfaces. We show that somatic variants in metastatic cases are more likely to be found in Pfam domains and protein interaction interfaces than are pathogenic germline variants or variants of unknown significance (VUS). We also show that there are hotspots in the structures of ATM and BRCA2 proteins where pathogenic germline, and recurrent somatic variants from primary and metastatic tumours, cluster together in 3D. Moreover, in the ATM, BRCA1 and BRCA2 genes from prostate cancer patients, the distributions of germline benign, pathogenic, VUS, and recurrent somatic variants differ across Pfam domains. Together, these results provide a better characterisation of the most recurrent affected regions in DDRs and could help in the understanding of individual susceptibility to tumour development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ataxia Telangiectasia Mutated Proteins / genetics
  • BRCA1 Protein / genetics
  • BRCA2 Protein / genetics
  • Computational Biology / methods*
  • DNA Damage
  • DNA Glycosylases / genetics
  • DNA Repair*
  • Genetic Predisposition to Disease*
  • Genetic Variation*
  • Germ-Line Mutation
  • Humans
  • Neoplasm Metastasis
  • Neoplasms / genetics*
  • Protein Domains
  • Protein Interaction Mapping


  • BRCA1 Protein
  • BRCA1 protein, human
  • BRCA2 Protein
  • BRCA2 protein, human
  • ATM protein, human
  • Ataxia Telangiectasia Mutated Proteins
  • DNA Glycosylases
  • mutY adenine glycosylase