Structural distance to the tRNA-synthetase binding interface predicts pathogenicity but is captured by AlphaMissense and EVE

Variants of uncertain significance have accumulated as genomic sequencing has become more widespread, which complicates rare disease diagnosis and requires substantial resources for re-evaluation. Aminoacyl-tRNA synthetases (ARSs) are a protein family with extensive variant data and well-characterized disease associations, making them an ideal system for investigating the relationship between variant location and pathogenicity. Using structural distance measurements to the ARS-tRNA binding interface combined with existing pathogenicity predictors, AlphaMissense and EVE, we investigated whether explicit structural binding information could improve missense variant pathogenicity prediction. Pathogenic variants were found to cluster significantly closer to the tRNA-binding interface than benign variants (p = 1.3e-09). Incorporating explicit distance information into a Bayesian mixture model did not substantially improve predictive performance over AlphaMissense and EVE alone. This suggests that these models already implicitly capture relevant structural binding context. However, a clinically important subset of interface variants classified as ambiguous by both existing models identifies a specific gap where explicit structural distance information may provide added discriminative value. However our analysis revealed that structural distance alone does not meaningfully contribute in prediction of pathogenicity for these variants. Incorporating additional biologically relevant features not captured by existing models, such as protein stability or conformational dynamics, as well as refining structural distance calculations, may further improve classification of this subset. These findings highlight both the power and the limitations of existing pathogenicity predictors and suggest that structurally informed approaches targeting the binding interface in addiition to other features represent a promising direction for improving classification of these ambiguous variants that have great clinical significance.