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

Area of Science:

• Genetics and Genomics
• Oncology
• Molecular Biology

Background:

• Germline pathogenic variants in Breast Cancer gene 1 (BRCA1) and BRCA2 significantly increase risks for breast, ovarian, and other cancers, defining hereditary breast and ovarian cancer (HBOC) syndrome.
• Accurate interpretation of BRCA1 and BRCA2 variants is crucial for patient management and family cancer risk assessment.
• The BRCA1:c.132C>T (p.Cys44=) synonymous variant has conflicting interpretations of pathogenicity in databases.

Purpose of the Study:

• To investigate the pathogenicity of the BRCA1:c.132C>T synonymous variant.
• To evaluate the variant's impact on splicing and protein function.
• To provide accurate genetic information for hereditary cancer risk assessment.

Main Methods:

• Clinical testing identified the BRCA1:c.132C>T variant in two early-onset breast cancer patients with ovarian involvement and family cancer history.
• Minigene assay was performed to assess the variant's effect on splicing.
• Reverse transcription-polymerase chain reaction (RT-PCR) analyzed RNA from patient blood samples.

Main Results:

• The minigene assay demonstrated that BRCA1:c.132C>T causes a four-nucleotide deletion in exon 3, leading to a truncated protein (p.Cys44Tyrfs*5).
• RT-PCR analysis confirmed aberrant splicing, consistent with minigene assay findings.
• The variant was classified as pathogenic based on functional studies, RNA analysis, and patient clinical and family histories.

Conclusions:

• BRCA1:c.132C>T (p.Cys44=) is a pathogenic variant contributing to hereditary breast and ovarian cancer.
• Synonymous variants at exon boundaries can impact splicing, a factor not always efficiently predicted by current in silico tools.
• Further research is needed to understand variants affecting gene expression and post-transcriptional modifications for improved BRCA1/BRCA2-related cancer insights.