Cell cycle checkpoint kinases activated by DNA repair pathways, ATM/Chk2 and ATR/Chk1 are important tumor suppressors. Germline mutations in these genes associate with increased cancer incidence. Specifically, ATM and CHEK2 germline variants associate with the incidence of estrogen receptor (ER)+ breast cancer with poor patient outcome. More recent investigations identified somatic inactivation of ATM/Chk2 as causal to endocrine therapy resistance in ER+ breast cancer patients. However, the relative contributions of germline and somatic inactivation of these cell cycle checkpoint kinases to ER+/HER2- and ER-/PR-/HER2- or triple negative breast cancer (TNBC) incidence and tumor characteristics has not been systematically assessed. Here, we comprehensively compare the association of ATM/CHEK2 and ATR/CHEK1 germline and somatic mutations with age, tumor stage and PR status at diagnosis, and metastatic potential using a meta-dataset compiled from six independent primary and metastatic patient datasets. We observe significantly higher frequency of ATM (*~29.6%) and CHEK2 (9.5%) mutations in metastatic ER+/HER2- breast cancers relative to TNBC (*~11% and 5% respectively)(p=0.03). CHEK2 mutations associate with higher PR positivity, higher tumor stage and younger age at diagnosis for metastatic ER+/HER2- breast cancer patients. These associations are primarily driven by germline, rather than somatic CHEK2 mutations. However, somatic CHEK2 mutations associate with more rapid disease progression on early rounds of endocrine therapy. These results provide the first systematic analysis of the contribution of germline and somatic cell cycle checkpoint kinase mutations to tumor characteristics affecting patient prognosis and treatment outcome. Results of this study suggest more streamlined use of the status of these checkpoint kinases as prognostic and/or predictive biomarkers for ER+/HER2- breast cancer patients.