Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms

Miguel De La Hoya, Omar Soukarieh, Irene López-Perolio, Ana Vega, Logan C. Walker, Yvette van Ierland, Diana Baralle, Marta Santamariña, Vanessa Lattimore, Juul T. Wijnen, Philip Whiley, Ana Blanco, Michela Raponi, Jan Hauke, Barbara Wappenschmidt, Alexandra Becker, Thomas V.O. Hansen, Raquel Behar, kConFab Investigators, Diether NiederacherNorbert Arnold, Bernd Dworniczak, Doris Steinemann, Ulrike Faust, Wendy Rubinstein, Peter J. Hulick, Claude Houdayer, Sandrine M. Caputo, Laurent Castera, Tina Pesaran, Elizabeth Chao, Carole Brewer, Melissa C. Southey, Christi J. Van Asperen, Christian F. Singer, Jan Sullivan, Nicola Poplawski, Pham Phuong Mai, Julian Peto, Nichola Johnson, Barbara Burwinkel, Harald Surowy, Stig E Bojesen, Henrik Flyger, Annika Lindblom, Sara Margolin, Jenny Chang-Claude, Anja Rudolph, Paolo Radice, Laura Galastri, Janet E Olson, Emily Hallberg, Graham G. Giles, Roger L Milne, Irene L Andrulis, Gord Glendon, Per Hall, Kamila Czene, Fiona Blows, Mitul Shah, Qin Wang, Joe Dennis, Kyriaki Michailidou, Lesley McGuffog, Manjeet K. Bolla, Antonis C Antoniou, Douglas F Easton, Fergus J Couch, Sean V. Tavtigian, Maaike P.G. Vreeswijk, Michael Parsons, Huong D. Meeks, Alexandra Martins, David E. Goldgar, Amanda B Spurdle

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64 Citations (Scopus)


A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A>C (IVS9-2A>C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A>C. The combined odds for causality considering case-control, segregation and breast tumor pathology information was 3.23 x 10-8. Our data indicate that c.594-2A>C is always in cis with c.641A>G. The spliceogenic effect of c.[594-2A>C;641A>G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A>C; 641A>G] caused exon 10 skipping, albeit not due to c.594-2A>C impairing the acceptor site but rather by c.641A>G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile composed of70-80% truncating transcripts, and20-30% of in-frame D9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function. We confirm that BRCA1c.[594-2A>C;641A>G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.

Original languageEnglish
Pages (from-to)2256-2268
Number of pages13
JournalHuman Molecular Genetics
Issue number11
Publication statusPublished - 1 Jun 2016
Externally publishedYes

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