Background/Objectives: MSH3 encodes a key component of the DNA mismatch repair (MMR) system, which is essential for maintaining genomic stability. Mutations in MSH3 have been associated with colorectal cancer (CRC), particularly within microsatellite instability and adenomatous polyposis syndromes. Beyond its oncogenic associations, MSH3 dysfunction has been linked to neurodegenerative disorders, such as Huntington’s disease, where impaired repair promotes trinucleotide repeat expansion. Despite its clinical relevance, the structural and pathogenic impact of MSH3 missense mutations remains insufficiently characterized. This study aims to systematically characterize the impact of all possible missense mutations in MSH3 on protein stability and predicted pathogenicity. Methods: Using the predicted AlphaFold structure, we conducted a saturated mutagenesis analysis of 21,603 MSH3 missense mutations. Folding energy changes (ΔΔG) were computed with FoldX, and pathogenicity was evaluated using Meta-SNP and AlphaMissense predictors. Clinically significant variants were cross-referenced from ClinVar, COSMIC, HGMD, and gnomAD databases. Results: Approximately 57.2% of variants destabilized MSH3 (ΔΔG > 0.5 kcal/mol), whereas 10.9% showed signs of stabilizing (ΔΔG < −0.5 kcal/mol). Notably, mutations G389W, G572W, G978W, G978Y, and G572Y introduced steric clashes that disrupted β-sheet packing, indicating conformational instability. Conversely, variations such as P64F, P64W, P64D, P6D, and P64R increased protein stability. Correlation analyses revealed partial agreement between predicted stability changes and pathogenicity scores, suggesting both structural and non-structural mechanisms underpinning disease risk. Conclusions: This comprehensive analysis defines the structural landscape of MSH3 missense mutations and identifies protein destabilization as a major contributor to variant pathogenicity. However, the incomplete concordance with predictive models indicates that additional non-structural mechanisms also influence disease risk. These findings provide a framework for interpreting MSH3 variants in cancer and neurodegenerative disorders and underscore the importance of integrating structural and functional evidence in variant classification.