MENDELSEEK: An algorithm that predicts mendelian genes and elucidates what makes them special

Abstract

Although individual Mendelian diseases—those caused by a single gene—are rare, their collective disease burden is substantial. Identifying the causal gene for each condition is essential for accurate diagnosis and effective treatment. Yet, despite decades of research, the genetic basis of more than half of all known Mendelian diseases remains unresolved. To address this gap, we introduce MENDELSEEK, a machine learning framework that predicts Mendelian genes by integrating residue variation scores with pathway participation, Gene Ontology processes, and protein language model features. In benchmarking across 16,946 human genes with 10-fold cross-validation, MENDELSEEK achieved an AUC of 0.869 and an AUPR of 0.737—substantially outperforming the next best methods, ENTPRISE+ENTPRISE-X (AUC 0.781; AUPR 0.626), and REVEL (AUC 0.585; AUPR 0.401). When applied to the full set of 17,858 human genes, MENDELSEEK predicted 1,277 novel Mendelian gene candidates with precision greater than 0.7. Analysis further revealed that Mendelian genes engage in significantly more protein-protein interactions than non-Mendelian genes and are evolutionarily ancient. Together, these results highlight MENDELSEEK as a major advance over existing methods, offering new insights into the biochemical features that distinguish Mendelian from non-Mendelian genes.