Deep Learning and Experimental Validation of BRCA1-Associated Protein-1 Missense Variant Pathogenicity in Uveal Melanoma

Objective: ) missense variants in uveal melanoma (UM). Design: Cross-sectional analytical study comparing computational predictions with experimentally derived functional classifications and clinical annotations. Subjects Participants and/or Controls: single amino acid substitutions profiled in a published Regularly Interspaced Short Palindromic Repeats-Cas9 SGE viability assay. No separate control cohort was required. Clinical Variant Database (ClinVar)-annotated variants within this set served as an independent reference. Prediction tools AlphaMissense, Rare Exome Variant Ensemble Learner (REVEL), Meta-predictor based on a Recurrent Neural Network (MetaRNN), and Combined Annotation Dependent Depletion (CADD) scores were aligned to SGE classifications. Diagnostic performance was assessed using receiver operating characteristic (ROC) and precision-recall (PR) analyses. Gene-specific threshold optimization for AlphaMissense was performed using Youden index. Structural mapping was performed using the AlphaFold2 BAP1 model. Main Outcome Measures: (1) Concordance between in silico predictors and SGE labels (area under ROC and PR curves); (2) agreement with ClinVar classifications; (3) structural clustering of high-risk residues. Results: missense variants, AlphaMissense predicted 8694 and 5816 as pathogenic by the genome-wide and optimized thresholds, respectively. Structural mapping highlighted clusters of high-risk substitutions within the catalytic core and protein-interaction motifs of the BAP1 protein. Finally, AlphaMissense predictions matched 11 of 12 ClinVar-classified variants (91.7%). This study introduces an optimized, gene-specific threshold that further enhances its precision, supporting the integration of artificial intelligence-based tools into ocular oncology precision-medicine pipelines for risk stratification and clinical decision-making. Financial Disclosures: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.