Comprehensive analysis of the functional impact of single nucleotide variants of humanCHEK2

Abstract

AbstractLoss of function mutations in the checkpoint kinase geneCHEK2are associated with increased risk of breast and other cancers. Most of the 3,188 unique amino acid changes that can result from non-synonymous single nucleotide variants (SNVs) ofCHEK2, however, have not been tested for their impact on the function of theCHEK2-enocded protein (CHK2). One successful approach to testing the function of variants has been to test for their ability to complement mutations in the yeast ortholog ofCHEK2,RAD53. This approach has been used to provide functional information on over 100CHEK2SNVs and the results align with functional assays in human cells and known pathogenicity. Here we tested all but two of the 4,887 possible SNVs in theCHEK2open reading frame for their ability to complementRAD53mutants using a novel high throughput technique. Among the non-synonymous changes, 770 were damaging to protein function while 2,417 were tolerated. The results correlate well with previous structure and function data and provide a first or additional functional assay for all the variants of uncertain significance identified in clinical databases. Combined, this approach can be used to help predict the pathogenicity ofCHEK2variants of uncertain significance that are found in patient screening and could be applied to other cancer risk genes.