BRCA2 NM_000059.3:c.7961T>C, Leu2654Pro

This missense variant replaces leucine with proline at codon 2654 of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant results in reduced or loss of homology-directed DNA repair activity (PMID: 23108138, 29394989). To our knowledge, this variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 1/31406 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The p.L2654P variant (also known as c.7961T>C), located in coding exon 16 of the BRCA2 gene, results from a T to C substitution at nucleotide position 7961. The leucine at codon 2654 is replaced by proline, an amino acid with similar properties. This variant is located in the DNA binding domain of BRCA2. This alteration was non-functional in a cell-based homology-directed DNA break repair (HDR) functional assay (Guidugli L et al. Cancer Res. 2013 Jan;73(1):265-75; Hart SN et al. Genet Med, 2019 01;21:71-80; Hu C et al. Am J Hum Genet. 2024 Mar;111(3):584-593). Two saturation genome editing-based studies, including a haploid cell-survival assay and a humanized mouse embryonic stem cell line assay of drug response and survival, demonstrate that this nucleotide substitution is non-functional(Huang H et al. Nature. 2025 Feb;638(8050):528-537; Sahu S et al. Nature. 2025 Feb;638(8050):538-545). This alteration is also predicted to destabilize the local structure and disrupt the protein binding ability of BRCA2 (Yang H et al. Science 2002 Sep;297:1837-48; Marston NJ et al. Mol. Cell. Biol. 1999 Jul;19:4633-42; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 2654 of the BRCA2 protein (p.Leu2654Pro). This variant is present in population databases (rs80359023, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with BRCA2-related conditions. ClinVar contains an entry for this variant (Variation ID: 52448). An algorithm developed specifically for the BRCA2 gene suggests that this missense change is likely to be deleterious (PMID: 19043619). Experimental studies have shown that this missense change affects BRCA2 function (PMID: 23108138, 29394989, 29884841, 35736817). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.