Clinical associations of functionally prioritized synonymous mutations: a pan-cancer analysis

Synonymous mutations are increasingly recognized as potentially functional, but their clinical relevance across cancer types remains uncertain. We evaluated functionally prioritized synonymous mutations across multiple cancers and their associations with clinical outcomes. We analyzed 8136 patients from 18 TCGA cancer cohorts. Synonymous mutations were prioritized using three predefined SynMICdb functional-score thresholds and summarized at the Cancer Gene Census gene level. Associations with survival outcomes were evaluated using multivariable Cox models and random-effects meta-analysis, with additional stage-adjusted and incremental model analyses. Transcriptomic correlates were assessed using gene-expression modeling and Hallmark enrichment analysis. Prioritized synonymous-mutation burden showed limited correlation with broader nonsynonymous mutation burden. No consistent pan-cancer association with overall or disease-specific survival was observed, whereas modest associations with progression-related outcomes occurred at broader thresholds. Cancer-specific effects were heterogeneous. Associations with poorer overall survival in liver hepatocellular carcinoma and with disease-free interval in ovarian cancer persisted after stage adjustment, although overall improvements in prognostic discrimination were limited. Transcriptomic profiles were highly concordant between the broader thresholds but showed cancer-dependent pathway associations without a common transcriptional signature. Functionally prioritized synonymous mutations show heterogeneous, context-dependent clinical and transcriptional associations across cancer types. Selected cancer-specific associations warrant further study, but the absence of a consistent pan-cancer effect and limited incremental prognostic performance do not support a general prognostic application.