PirePred: An Accurate Online Consensus Tool to Interpret Newborn Screening-Related Genetic Variants in Structural Context.

PirePred is a genetic interpretation tool used for a variety of medical conditions investigated in newborn screening programs. The PirePred server retrieves, analyzes, and displays in real time genetic and structural data on 58 genes/proteins associated with medical conditions frequently investigated in the newborn. PirePred analyzes the predictions generated by 15 pathogenicity predictors and applies an optimized majority vote algorithm to classify any possible nonsynonymous single-nucleotide variant as pathogenic, benign, or of uncertain significance. PirePred predictions for variants of clear clinical significance are better than those of any of the individual predictors considered (based on accuracy, sensitivity, and negative predictive value) or are among the best ones (for positive predictive value and Matthews correlation coefficient). PirePred predictions also outperform the comparable in silico predictions offered as supporting evidence, according to American College of Medical Genetics and Genomics guidelines, by VarSome and Franklin. Also, PirePred has very high prediction coverage. To facilitate the molecular interpretation of the missense, nonsense, and frameshift variants in ClinVar, the changing amino acid residue is displayed in its structural context, which is analyzed to provide functional clues. PirePred is an accurate, robust, and easy-to-use tool for clinicians involved in neonatal screening programs and for researchers of related diseases. The server is freely accessible and provides a user-friendly gateway into the structural/functional consequences of genetic variants at the protein level.