Intronic alterations in BRCA1 and BRCA2:: Effect on mRNA splicing fidelity and expression

Germline mutations in the human breast cancer susceptibility genes BRCA1 and BRCA2 account for the majority of hereditary breast and ovarian cancer. In spite of the large number of sequence variants identified in BRCA1 and BRCA2 mutation analyses, many of these genetic alterations are still classified as variants of unknown significance (VUS). In this study, we evaluated 12 BRCA1/2 intronic variants in order to differentiate their pathogenic or polymorphic effects on the mRNA splicing process. We detected the existence of aberrant splicing in three BRCA1 variants (c.301-2delA/IVS6-2delA, c.441+1G > A/IVS7+IG > A, and c.4986+ 6T > G/IVS16+6T > G) and two BRCA2 variants (c.8487+1G > A/IVS19+1G > A and c.8632-2A > G/IVS20-2A > G). All but one of the aberrant transcripts arise from mutations affecting the conserved splice acceptor or donor sequences and all would be predicted to result in expression of truncated BRCA1 or BRCA2 proteins. However, we demonstrated that four of these splice-site mutations (i.e., c.301-2delA, c.441+1G > A, c.4986+6T > G, and c.8632-2A > G) with premature termination codons were highly unstable and were unlikely to encode for abundant expression of a mutant protein. Three variants of BRCA1 (c.212+3A > G/ IVS5+3A > G, c.593+8A > G/IVS9+8A > G, and c.4986-20A > G/IVS16-20A > G) and four variants of BRCA2 (c.516,19C > T/IVS6-19C > T, c.7976_47976_3delTT/IVS17-4deITT, c-8487+19A > G/IVS19+ 19A > G, and c.9256,18C > A/IVS24-18C > A) in our studies show no effects on the normal splicing process, and they are considered to be benign polymorphic alterations. Our studies help to clarify the aberrant splicing in BRCA1 and BRCA2 as well as provide information that can be used clinically to help counsel breast/ovarian cancer prone families.