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Background  We evaluated the incidence and spectrum of pathogenic and likely pathogenic variants of cancer susceptibility genes in  BRCA1/2  mutation-negative Korean patients with a high risk for hereditary breast cancer using a comprehensive multigene panel that included 35 cancer susceptibility genes.    Methods  Samples from 120 patients who were negative for  BRCA1/2  mutations, but had been diagnosed with breast cancer that was likely hereditary, were prospectively evaluated for the prevalence of high-penetrance and moderate-penetrance germline mutations.    Results  Nine patients (7.5%) had at least one pathogenic or likely pathogenic variant. Ten variants were identified in these patients:  TP53  in two patients,  PALB2  in three patients,  BARD1  in two patients,  BRIP1  in two patients, and  MRE11A  in one patient. We also identified 30 types of 139 variants of unknown significance (VUS). High-penetrance germline mutations, including  TP53  and  PALB2,  tended to occur with high frequency in young (< 35 years) breast cancer patients (4/19, 21.1%) than in those diagnosed with breast cancer at ≥35 years of age (1/101, 1.0%;  p  = 0.003).    Conclusions  These combined results demonstrate that multigene panels offer an alternative strategy for identifying veiled pathogenic and likely pathogenic mutations in breast cancer susceptibility genes.    Electronic supplementary material  The online version of this article (10.1186/s12885-017-3940-y) contains supplementary material, which is available to authorized users.

Variants of cancer susceptibility genes in Korean BRCA1/2 mutation-negative patients with high risk for hereditary breast cancer