Mundt, Erin

Abstract Background: BRCA2 variants with partially aberrant RNA splicing have been associated with a relatively lower breast cancer risk (reduced penetrance) relative to canonical pathogenic variants. However, the existence of partial loss of function (hypomorphic) missense variants, conferring reduced penetrance, is less certain. Identification and assessment of the clinical relevance of such reduced penetrance pathogenic variants (RPPVs) is needed to provide accurate risk estimates. Methods: Comprehensive functional characterization of hypomorphic missense variants (n=70) in the BRCA2 DNA-binding domain, initially identified through homology-directed DNA repair (HDR) assays, was conducted through multiple independent functional assays, including HDR, CRISPR/Cas9-based endogenous targeting, RAD51 foci formation assay, and Poly(ADP-ribose) polymerase (PARP) inhibitor response assay. Risk estimates were obtained using two large datasets from patients referred for hereditary cancer testing. A ClinGen/ACMG/AMP model was used for clinical classification. Results: The variants consistently demonstrated hypomorphic HDR activity and endogenous survival in HAP1 targeted cells, decreased RAD51 foci formation, and increased sensitivity to PARP inhibitors. These variants were associated with a moderate increase in breast cancer risk, as shown in two independent studies: one using multivariable logistic analysis adjusted for age, ancestry and family history (OR=2.41, 95%CI=1.51-3.85) and another comparing frequencies of variants in breast cancer cases to public reference controls adjusted for ancestry (OR=2.09, 95% CI=1.16-4.08). The mean age of breast cancer diagnosis for carriers of hypomorphic variants was 57 years, which was significantly older than the mean age of diagnosis of 51 years for carriers of protein truncating variants. Functional data were combined with other evidence sources in a ClinGen/ACMG/AMP model to classify 14 variants as “likely pathogenic”. Conclusions: We identified partially functional, hypomorphic missense variants associated with reduced penetrance for breast cancer. Cancer risk management guidelines for this new category of variants should be revisited given that the associated breast cancer risks warrant high risk screening but do not meet the threshold at which risk reducing mastectomy is offered. This study supports a shift in paradigm to considering variant-based risks on a continuum, with implications for risk-appropriate cancer risk management. Citation Format: H. Huang, C. Hu, J. Na, M. Kucera, T. Simmons, E. Mundt, C. C. Young, Z. Heidari, P. C. Lyra, Y. Y. Tan, K. L. Nathanson, T. Pal, R. Karam, T. Pesaran, S. Yadav, S. M. Domchek, A. N. Monteiro, E. Hughes, N. Boddicker, W. Chen, M. E. Richardson, F. J. Couch. Partially functional (hypomorphic) missense variants in BRCA2 are reduced penetrance pathogenic variants [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PD4-05.

Abstract Despite the current binary clinical classification of variants (pathogenic versus benign), it is widely recognized that risk is a continuum. Prior studies have suggested the existence of reduced penetrance pathogenic variants (RPPVs), which pose challenges for identification, reporting, patient counseling and care. Through the current study, we sought to establish RPPVs as a new category of variants, with efforts focused specifically on BRCA1 and BRCA2 (BRCA). We compiled, compared, and assessed data for BRCA RPPVs from two large clinical diagnostic laboratories to establish an initial set of reduced penetrance pathogenic variants. Specifically, candidate BRCA RPPVs provided by clinical diagnostic laboratories were compiled to identify those with the highest prior likelihood of being a RPPV, based on concordant interpretations. Evidence of reduced penetrance included: 1) the identification of biallelic Fanconi Anemia-affected carriers; 2) splicing, missense, and nonsense-mediated RNA decay (NMD)-escaping variants; 3) laboratory-validated cancer history weighting models; 4) published variant-specific risk estimation data; 5) extrapolation of a reduced-risk interpretation onto close match variants that are expected to have the same effect; and 6) functional data. Sixteen candidate BRCA RPPV present in both lists from both laboratories were systematically assessed. For BRCA1, variants included c.5096G>A p.(Arg1699Gln) and variants impacting the canonical c.671 splice acceptor site. For BRCA2, variants included three frameshift (c.658_658delGT, c.9672dupA, c.9699_9702delTATG), two spliceogenic (c.8488-1G>A and c.8488-1G>T), and three missense (c.7878G>C, T, p.(Trp2626Cys); and c.9302T>G p.(Leu3101Arg)) variants. Our study is the first to clearly evaluate and establish BRCA RPPVs as a new class of variants, based on consistency in results across 16 variants using different interpretation strategies between laboratories. These variants impart a moderately increased risk of breast cancer, often considered to be between 2-4 fold, which should be considered when determining risk-informed cancer prevention strategies. Furthermore, our study establishes a framework to harmonize interpretation and standardize reporting of BRCA RPPV, by providing evidence to support this new classification for 16 variants. Further work to define clinically meaningful risk thresholds and categories for reporting BRCA RPPV are needed to personalize cancer risks in conjunction with other risk factors. Citation Format: Tuya Pal, Erin Mundt, Marcy Richardson, Elizabeth Chao, Tina Pesaran, Thomas P. Slavin, Fergus Couch, Alvaro N. Monteiro. Reduced penetrance BRCA1 and BRCA2 pathogenic variants in clinical germline genetic testing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6615.