A comprehensive functional landscape of α-tubulin TUBA1A variants illuminates microtubule biology and refines clinical classification

Missense variant interpretation in highly conserved, paralog-rich gene families remains a critical bottleneck for precision medicine. Here, we developed an integrated experimental-computational platform to systematically assess the functional impact of all possible missense mutations in the α-tubulin TUBA1A. Combining high-throughput comprehensive mutagenesis, high-content imaging, convolutional neural network– driven phenotyping, and machine learning–guided prediction, we quantified microtubule assembly phenotypes for every coding variant. This approach outperforms conservation-based predictors and enables functional reinterpretation of disease-associated variants. Structural mapping of the TUBA1A mutational landscape reveals distinct domains critical for GTP binding, chaperone-assisted folding or protofilament interaction, illuminating diverse mechanisms of tubulin-related diseases. Integration with ACMG-AMP guidelines demonstrates this mutational landscape improves clinical variant classification in redundant gene families. This framework is broadly applicable to other structurally conserved proteins, linking variant effect prediction to mechanistic insight and clinical translation.