Atypical cancer risk profile in carriers of Italian founder BRCA1 variant p.His1673del: Implications for classification and clinical management

Abstract

Background: BRCA1:c.5017_5019del (p.His1673del) is a founder variant relatively frequent in Northern Italy. Despite previous suggestion of pathogenicity, variant classification in public databases is still conflicting, needing additional evidence.

Methods: Maximum likelihood penetrance of breast/ovarian and other cancer types was estimated using full pedigree data from 53 informative Italian families. The effect of the variant on BRCA1-ABRAXAS1 interaction was assessed using a GFP-fragment reassembly-based PPI assay. Results were combined with additional data from multiple sources to classify the variant according to ACMG/AMP classification rules specified for BRCA1/2.

Results: Variant-carriers displayed increased risk for ovarian cancer (HR = 33.0, 95% CI = 7.0-155.0; cumulative risk at age 70 = 27.6%, 95% CI = 12.6-40.0%) but not for breast cancer (HR = 0.7, 95% CI = 0.2-2.2). An increased risk of uterine cancer (HR = 8.0, 95% CI = 1.03-61.6) emerged, warranting further evaluation. Likelihood-ratio in favor of pathogenicity was 98898642.82 under assumption of standard BRCA1 breast and ovarian penetrance, and 104240832.84 after excluding breast cancer diagnoses (based on penetrance results). Functional analysis demonstrated that the variant abrogates the BRCA1-ABRAXAS1 binding, supporting the PS3 code assignment within the ACMG/AMP rule-based model. Collectively, these findings allowed to classify the variant as pathogenic.

Conclusion: Pathogenicity of BRCA1:c.5017_5019del(p.His1673del) has been confirmed; however, breast cancer risk in Italian families is not increased, unlike in families from other countries and in carriers of most BRCA1 pathogenic variants. The knowledge of atypical risk profiles for this and other variants will pave the way for personalized management based on specific genotype.

Keywords: BRCA1; breast cancer; cancer risk; classification; clinical management; ovarian cancer; penetrance; uterine cancer.

FIGURE 1

Cumulative risk (%) estimates for breast, ovarian and uterine cancer in female Italian carriers of c.5017_5019del (p.His1673del) variant. Estimates were calculated assuming a constant HR across age groups, with simultaneous analysis for BC and OC, and with independent analysis for UC.

FIGURE 2

Detection of the BRCA1‐ABRAXAS1 interaction. (A) In vitro GFP‐reassembly assays. Fluorescence was recovered, under long‐wave UV light (365 nm), after 24 h of growth at 37°C followed by 3 days of incubation at room temperature. Arctic Express (D3) E.coli bacterial cells were co‐transformed twice with each compatible pair of plasmids. C‐: Arctic Express (D3) E.coli bacterial cells co‐expressing non‐cognate BRCA1 and Leucine zipper fusion pepetides as negative control. (B) Analysis of expression of BRCA1‐NfrGFP and ABRAXAS1‐CfrGFP wild‐type and mutant forms. Cell extracts from the co‐transformed ArcticExpress (DE3) E. coli cells were subjected to SDS‐PAGE and visualized by Western blotting using a polyclonal anti‐GFP antibody.