Significance Many therapeutic strategies are hampered by the development of drug resistance. High-throughput random mutagenesis screens represent a promising approach for identifying mutations that lead to drug resistance, but have often identified more resistant mutations than are observed in patients, raising questions of their clinical significance. We developed an improved high-throughput mutagenesis screening approach that uses CRISPR-Cas9–based genome editing to generate comprehensive libraries of point mutations at a defined genomic location and systematically study their effect on cell growth. As proof-of-concept, we show our approach accurately predicts the clinical prevalence of drug-resistant mutations in the oncogene BCR-ABL . Our approach can be broadly applied to a variety of oncogenes and represents a new strategy for evaluating resistance susceptibility during drug development.