Modeling the Effects of Single Nucleotide Polymorphisms (SNPs) on the Structure and Function of the Human RET Gene: An In Silico Study.

The RET proto-oncogene plays a critical role in multiple cancers and developmental disorders, where nonsynonymous single nucleotide polymorphisms (nsSNPs) may alter protein stability, function, and therapeutic response. In this study, a total of 28,335 SNPs from the NCBI dbSNP database, including 2377 nsSNPs, were systematically analyzed using 10 in silico prediction tools. Among these 33 high-risk variants were identified with 28 predicted to destabilize RET protein. Further structural and functional analyses highlighted 11 potentially pathogenic nsSNPs (R721G, A756D, Y791C, E734K, E805K, F893L, R897Q, R897G, R912Q, R912G, and M918T), predominantly clustered within the tyrosine kinase domain, suggesting functional hotspots may contribute disease susceptibility. Molecular docking of eight RET inhibitors revealed mutation-specific differences in drug binding affinity. Among the tested compounds, entrectinib exhibited consistently strong binding affinities across all variants (-9.7 to -10.7 kcal/mol), whereas reduced binding affinities were observed for several inhibitors against E734K, A756D, and R897G variants. Molecular dynamics simulations further supported these findings, showing that A756D, E734K, and R897Q variants maintained comparatively stable conformations, whereas R897G and Y791C exhibited increased structural flexibility and destabilization. Survival analyses revealed that RET dysregulation correlates with poor prognosis in thyroid cancer, lung carcinoma, breast cancer, and sarcoma. Clinical databases reported that p.Met918Thr (pathogenic) and p.Arg897Gln (risk factor) emerged as significant variants linked to MEN2-related cancers and Hirschsprung disease. As a conclusion, this integrative in silico study identifies deleterious RET nsSNPs with potential structural, functional, and therapeutic significance providing mechanisms for precision oncology and future clinical investigation.