In summary, we identified molecular subtype-specific novel prognostic genes in breast cancer and developed a novel prognostic model to predict the risk of distant metastasis for HR−/HER2+ breast cancer based on the gene expression of MMP11 and CD2. Our prognostic model was superior to traditional clinicopathological factors in prognostic performance and may be used in identifying patients with good prognosis from this aggressive subtype of breast cancer. Here, MMP11 is linked to breast cancer.