FDPSM: Feature-Driven Prediction Modeling of Pathogenic Synonymous Mutations

Synonymous mutations, once considered to be biologically neutral, are now recognized to affect protein expression and function by altering the RNA splicing, stability, or translation efficiency. These effects can contribute to disease, making the prediction of the pathogenicity a crucial task. Computational methods have been developed to analyze the sequence features and biological functions of synonymous mutations, but existing methods face limitations, including scarcity of labeled data, reliance on other prediction tools, and insufficient representation of feature interrelationships. Here, we present FDPSM, a novel prediction method specifically designed to predict pathogenic synonymous mutations. FDPSM was trained on a robust data set of 4251 positive and negative training samples to enhance predictive accuracy. The method leveraged a comprehensive set of features, including genomic context, conservation, splicing effects, functional effects, and epigenomics, without relying on prediction scores from other mutation pathogenicity tools. Recognizing that original features alone may not fully capture the distinctions between pathogenic and benign synonymous mutations, we enhanced the feature set by extracting effective information from the interactions and distribution of these features. The experimental results showed that FDPSM significantly outperformed existing methods in predicting the pathogenicity of synonymous mutations, offering a more accurate and reliable tool for this important task. FDPSM is available at https://github.com/xialab-ahu/FDPSM.