Objective To analyze ethnic differences in hotspot mutations of the PIK3CA and TP53 genes among breast cancer patients from the Han, Tibetan, and Hui ethnic groups in Qinghai, China, and their associations with clinicopathological characteristics.

Methods A total of 382 breast cancer tissue samples were retrospectively collected from surgical patients (June 2022–May 2023), comprising 200 Han, 93 Tibetan, and 89 Hui ethnicity. Mutations in PIK3CA (E542K, H1047R, and E545K) and TP53 (R273H and R175H) were detected by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Correlations between mutations and clinicopathological parameters were analyzed.

Results Significant differences were observed in pTNM stage, lymph node metastasis, molecular subtypes, and PR status among the three ethnic groups. The overall mutation rate of PIK3CA and TP53 was 48.95%. The PIK3CA-p.E542K mutation rate in Tibetan cohort was significantly higher than those in Han and Hui cohort, whereas the detection rate of the PIK3CA-p.E545K mutation was lower in Tibetan cohort than that in Han cohort. The PIK3CA-p.E542K mutation was associated with an increased risk of lymph node metastasis. The TP53-p.R175H mutation was significantly correlated with advanced pTNM stage, vascular invasion, and triple-negative breast cancer. The PIK3CA-H1047R and E545K mutations were enriched in the luminal A subtype of breast cancer.

Conclusion Considerable ethnic disparities exist in breast cancer mutation profiles in Qinghai, with the high-frequency PIK3CA-p.E542K mutation in Tibetan population potentially serving as a region-specific therapeutic target. Mutations are closely linked to tumor aggressiveness and molecular subtypes, highlighting the value of PIK3CA/TP53 mutation detection for early risk stratification and personalized treatment of breast cancer in high-altitude populations.