Background Clinical classification of rare sequence changes identified in the breast cancer susceptibility genes BRCA1 and BRCA2 is essential for appropriate genetic counselling of individuals carrying these variants. We previously showed that variant BRCA1 c.5096G>A p.Arg1699Gln in the BRCA1 transcriptional transactivation domain demonstrated equivocal results from a series of functional assays, and proposed that this variant may confer low to moderate risk of cancer.
Methods Measures of genetic risk (report of family history, segregation) were assessed for 68 BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) families recruited through family cancer clinics, comparing results with 34 families carrying the previously classified pathogenic BRCA1 c.5095C>T p.Arg1699Trp (R1699W) mutation at the same residue, and to 243 breast cancer families with no BRCA1 pathogenic mutation (BRCA-X).
Results Comparison of BRCA1 carrier prediction scores of probands using the BOADICEA risk prediction tool revealed that BRCA1 c.5096G>A p.Arg1699Gln variant carriers had family histories that were less ‘BRCA1-like’ than BRCA1 c.5095C>T p.Arg1699Trp mutation carriers (p<0.00001), but more ‘BRCA1-like’ than BRCA-X families (p=0.0004). Further, modified segregation analysis of the subset of 30 families with additional genotyping showed that BRCA1 c.5096G >A p.Arg1699Gln had reduced penetrance compared with the average truncating BRCA1 mutation penetrance (p=0.0002), with estimated cumulative risks to age 70 of breast or ovarian cancer of 24%.
Conclusions Our results provide substantial evidence that the BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) variant, demonstrating ambiguous functional deficiency across multiple assays, is associated with intermediate risk of breast and ovarian cancer, highlighting challenges for risk modelling and clinical management of patients of this and other potential moderate-risk variants.
- Cancer: breast
- Genetic epidemiology
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Funding This work was supported in part by project grants from The National Health and Medical Research Council (NHMRC) to ABS. ABS is supported by an NHMRC Senior Research Fellowship. kConFab is supported by grants from the National Breast Cancer Foundation, the NHMRC and by the Queensland Cancer Fund, the Cancer Councils of New South Wales, Victoria, Tasmania and South Australia, and the Cancer Foundation of Western Australia. The kConFab Clinical Follow Up Study was funded by NHMRC grants (145684 and 288704). BJF is supported by the Canadian Institutes of Health Research Team Grant in Familial Risks of Breast Cancer CRN-87521. AL thanks the Swedish Cancer Society for support. The work of the German Consortium GC-HBOC is supported by a grant of the German Cancer Aid (grant 107364, RKS) and by the Centre for Molecular Medicine Cologne, Cologne, Germany (RKS, BW). The French Consortium thanks the Association d'Aide à la Recherche Cancérologique de Saint Cloud (ARCs) and the Ligue 92 contre le Cancer for their financial support. FJC and DEG are supported by NIH grant CA116167, an NIH Recovery Act supplement (CA116167Z), and an NIH Specialised Programme of Research Excellence (SPORE) in Breast Cancer (CA116201). LG is supported by a Komen Race for the Cure Fellowship. Research by TvOH was supported by the NEYE Foundation. SMD is supported by funding from the Komen Foundation for the Cure. Ohio State University CCG is supported by the OSU Comprehensive Cancer Center (AET). EJVR is funded by grants from the Cancer Association of South Africa. The research coordinated by MPGV was supported by Dutch Cancer Society grants 2001-2471 and 2006-3677. DEG is supported by NIH grant CA116167. Coordination of ENIGMA is funded by The National Institutes of Health Recovery Act supplement award (CA116167Z).
Competing interests None.
Provenance and peer review Not commissioned; externally peer reviewed.