Abstract:Background and Aims The BRAFV600E mutation is the most common genetic alteration in papillary thyroid carcinoma (PTC) and is widely used to guide surgical extent and risk stratification. However, other genetic variants are increasingly identified in clinical practice, and their association with lymph node metastasis (LNM) remains unclear. Most existing studies have compared BRAFV600E-mutated cases with BRAF wild-type cases without stratifying specific mutation types, potentially affecting the accuracy of risk assessment. This study aimed to compare the lymph node metastatic features between PTC patients with different common genetic alterations and those with the BRAFV600E mutation.Methods A retrospective analysis was conducted on 4 795 PTC patients who underwent surgery and genetic testing at Fudan University Shanghai Cancer Center from January 2019 to January 2025. Patients with a single genetic alteration were included and grouped accordingly. Propensity score matching (PSM) was used to control for confounding factors including age, sex, and T stage. The number of metastatic lymph nodes and N stage were compared between each mutation group and the BRAFV600E group.Results After PSM, patients in the CCDC6-RET and NCOA4-RET fusion groups had significantly higher numbers of metastatic lymph nodes and N1b stage rates compared to the BRAFV600E group (all P<0.05). No significant differences were observed between the ETV6-NTRK3 fusion or RAS mutation groups and the BRAFV600E group in terms of lymph node metastasis or N stage (all P>0.05).Conclusion PTC patients harboring CCDC6-RET or NCOA4-RET fusions exhibit a significantly higher lymph node metastatic burden than those with the BRAFV600E mutation, suggesting more aggressive behavior. In contrast, ETV6-NTRK3 and RAS-mutated PTCs show similar metastatic profiles to BRAFV600E-mutated cases. Preoperative genetic profiling may help identify patients at high risk of metastasis and guide individualized lymph node dissection strategies.