Reclassification of ATM Missense Variants of Uncertain Significance by Integrating Results from Systematic Functional Assays into an ACMG Points-Based Framework.

Abstract

ATM is a moderate-risk cancer susceptibility gene that harbors thousands of missense variants of uncertain significance (VUS) which limit the power of clinical genetic testing for cancer risk management and personalized medicine. Functional tests provide a valuable basis for testing the impact of variants but have been lacking for ATM. We developed a systematic approach to functionally characterize missense ATM variants based on the correction of various DNA damage-related phenotypes via reexpression of ATM in either of two ATM-deficient human cell lines. A pKAP1 phospho-flow assay for ATM VUS observed in patients with hereditary cancer was calibrated using 48 benign and pathogenic controls, achieving 100% specificity and 97% sensitivity. This system distinguished 82 of 88 (93%) missense ATM VUS of the FATKIN region as functionally neutral or deleterious. Importantly, for the clinical classification of VUS, functional results were incorporated into an American College of Medical Genetics points-based framework, also considering conservation and properties of amino acids/substitutions, along with genetic data; 79 of 88 (90%) were thereby reclassified as benign/likely benign or pathogenic/likely pathogenic. As additional validation of our approach, clinical characteristics from a database of 1,134 patients with breast cancer were distinct for carriers of neutral versus deleterious ATM variants. Also, utilizing our functional results, we identified hotspots for deleterious VUS and controls at amino acids 2702-2730 and 2891-2951 of ATM. We have established functional assays as a reliable tool that will better interpret the clinical impact of ATM variants and guide improved cancer prevention measures for carriers.