Characterization of Synonymous BRCA1:c.132C>T as a Pathogenic Variant

Jun Li; Ping Wang; Cuiyun Zhang; Sile Han; Han Xiao; Zhiyuan Liu; Xiaoyan Wang; Weiling Liu; Bing Wei; Jie Ma; Hongle Li; Yongjun Guo

doi:10.3389/fonc.2021.812656

Characterization of Synonymous BRCA1:c.132C>T as a Pathogenic Variant

Front Oncol. 2022 Jan 11:11:812656. doi: 10.3389/fonc.2021.812656. eCollection 2021.

Authors

Jun Li^{1

2

3}, Ping Wang⁴, Cuiyun Zhang^{1

2

3}, Sile Han¹, Han Xiao⁵, Zhiyuan Liu⁶, Xiaoyan Wang^{1

2

3}, Weiling Liu⁷, Bing Wei^{1

2

3}, Jie Ma^{1

2

3}, Hongle Li¹, Yongjun Guo^{1

2

3}

Affiliations

¹ Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.
² Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.
³ Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China.
⁴ Department of Pathophysiology, School of Basic Medical Science, Zhengzhou University, Zhengzhou, China.
⁵ Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
⁶ Amoy Diagnostics Co., Ltd. (AmoyDx), Xiamen, China.
⁷ Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzou, China.

Abstract

Breast cancer gene 1 (BRCA1) and BRCA2 are tumor suppressors involved in DNA damage response and repair. Carriers of germline pathogenic or likely pathogenic variants in BRCA1 or BRCA2 have significantly increased lifetime risks of breast cancer, ovarian cancer, and other cancer types; this phenomenon is known as hereditary breast and ovarian cancer (HBOC) syndrome. Accurate interpretation of BRCA1 and BRCA2 variants is important not only for disease management in patients, but also for determining preventative measures for their families. BRCA1:c.132C>T (p.Cys44=) is a synonymous variant recorded in the ClinVar database with "conflicting interpretations of its pathogenicity". Here, we report our clinical tests in which we identified this variant in two unrelated patients, both of whom developed breast cancer at an early age with ovarian presentation a few years later and had a family history of relevant cancers. Minigene assay showed that this change caused a four-nucleotide loss at the end of exon 3, resulting in a truncated p.Cys44Tyrfs*5 protein. Reverse transcription-polymerase chain reaction identified two fragments (123 and 119 bp) using RNA isolated from patient blood samples, in consistency with the results of the minigene assay. Collectively, we classified BRCA1:c.132C>T (p.Cys44=) as a pathogenic variant, as evidenced by functional studies, RNA analysis, and the patients' family histories. By analyzing variants recorded in the BRCA Exchange database, we found synonymous changes at the ends of exons could potentially influence splicing; meanwhile, current in silico tools could not predict splicing changes efficiently if the variants were in the middle of an exon, or in the deep intron region. Future studies should attempt to identify variants that influence gene expression and post-transcription modifications to improve our understanding of BRCA1 and BRCA2, as well as their related cancers.

Keywords: BRCA1/2; HBOC; splicing variants; synonymous variants; variants classification.