In summary, our study confirms a nonlinear dose–response relationship between BRAF V600E mutation abundance and the risk of lymph node metastasis in PTC, with an abundance threshold of approximately 20.7% being associated with a markedly increased metastasis risk; a machine learning model that combines mutation abundance with clinical features can effectively predict lymph node metastasis risk, with good interpretability and potential clinical applicability. The gene discussed is BRAF; the disease is metastatic malignant neoplasm in the lymph nodes.