Background: The increasing use of multigene germline testing in breast cancer has expanded the detection of pathogenic/likely pathogenic (P/LP) variants and variants of uncertain significance (VUSs) across a broad range of breast cancer susceptibility genes. However, the extent to which pathogenic certainty and penetrance level are associated with distinct clinicopathological phenotypes and management patterns remains incompletely defined. Methods: In this multicenter retrospective study, we included 405 breast cancer patients with germline alterations in breast cancer susceptibility genes. Patients were classified into three groups: high-penetrance P/LP (
n = 116), moderate/low-penetrance P/LP (
n = 69), and VUS (
n = 220). The primary endpoint was non-luminal invasive breast cancer phenotype, defined as HER2-positive or triple-negative disease versus luminal A/B disease. Multivariable logistic regression was performed to assess the association between genetic group and non-luminal phenotype, adjusted for age at diagnosis and family history. Secondary analyses evaluated management patterns across groups and examined a prespecified non-
BRCA cohort. Results: Patients with high-penetrance P/LP variants were younger at diagnosis and had higher Ki-67 values than those in the other groups. Molecular subtype distribution differed significantly across groups, with triple-negative disease most frequent in the high-penetrance P/LP group (33.9%) compared with the moderate/low-penetrance P/LP (9.8%) and VUS (12.9%) groups. In multivariable analysis, high-penetrance P/LP status was independently associated with increased odds of non-luminal phenotype compared with VUS (OR 1.79, 95% CI 1.06–3.04;
p = 0.029), whereas moderate/low-penetrance P/LP status was not (OR 0.96, 95% CI 0.48–1.91;
p = 0.911). Management patterns also differed significantly. Initial mastectomy was performed in 65.4% of evaluable patients in the high-penetrance P/LP group, compared with 46.4% in the moderate/low-penetrance P/LP group and 45.5% in the VUS group. Final bilateral mastectomy was observed in 62.6%, 17.5%, and 9.9%, respectively (
p < 0.001). In the prespecified non-
BRCA analysis, non-
BRCA P/LP status was not associated with non-luminal phenotype compared with non-
BRCA VUS (OR 0.83, 95% CI 0.40–1.72;
p = 0.609). Conclusions: Among breast cancer patients with germline alterations in breast cancer susceptibility genes, high-penetrance P/LP variants are associated with a distinct clinicopathological profile characterized by younger age at diagnosis, higher proliferative activity, and increased likelihood of non-luminal disease. In contrast, moderate/low-penetrance P/LP variants, especially VUSs, do not show the same degree of phenotype specificity. These findings support a framework in which pathogenic certainty and penetrance level remain central to the interpretation of multigene germline testing in breast cancer.
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