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Background   FANCM  and  RECQL  have recently been reported as breast cancer susceptibility genes and it has been suggested that they should be included on gene panel tests for breast cancer predisposition. However, the clinical value of testing for mutations in  RECQL  and  FANCM  remains to be determined. In this study, we have characterised the spectrum of  FANCM  and  RECQL  mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine.    Methods  We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron-exon junctions of  FANCM  and  RECQL  in germline DNA from unrelated women affected with breast cancer ( n  = 338) and ovarian cancer ( n  = 89) from Poland ( n  = 304) and Ukraine ( n  = 123). These women were at high-risk of carrying a genetic predisposition to breast and/or ovarian cancer due to a family history and/or early-onset disease.    Results  Among 427 women screened, we identified one carrier of the  FANCM: c.1972C > T nonsense mutation (0.23%), and two carriers of the frameshift insertion  FANCM: c.1491dup (0.47%). None of the variants we observed in  RECQL  were predicted to be loss-of-function mutations by standard variant effect prediction tools.    Conclusions  Our study of the Polish and Ukrainian populations has identified a carrier frequency of truncating mutations in  FANCM  consistent with previous reports. Although initial reports suggesting that mutations in  RECQL  could be associated with increased breast cancer risk included women from Poland and identified the  RECQL: c.1667_1667 + 3delAGTA mutation in 0.23–0.35% of breast cancer cases, we did not observe any carriers in our study cohort. Continued screening, both in research and diagnostic settings, will enable the accumulation of data that is needed to establish the clinical utility of including  RECQL  and  FANCM  on gene panel tests.    Electronic supplementary material  The online version of this article (10.1186/s12881-018-0524-x) contains supplementary material, which is available to authorized users.

FANCM and RECQL genetic variants and breast cancer susceptibility: relevance to South Poland and West Ukraine