BRCA2 NM_000059.4:c.8023A>G, Ile2675Val

Variant summary: BRCA2 c.8023A>G (p.Ile2675Val) results in a conservative amino acid change located in the BRCA2, OB1 domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Three predict that the variant creates a cryptic exonic 5-prime donor site. These predictions were confirmed by experimental evidence which demonstrated that the variant results in loss of a stretch of 309 nucleotides at the 3-prime terminal of exon 18 from the mRNA. Multiple studies observed abundant aberrant product and a complete absence of wild type product (Fraile-Bethencourt_2017, Houdayer_2012, Bonnet_2008). The variant allele was found at a frequency of 4e-06 in 251076 control chromosomes. c.8023A>G has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (e.g. Rebbeck_2018, Hirotsu_2015, Blay_2013, Bonnet_2008, Palma_2008). These data indicate that the variant is very likely to be associated with disease. Six other ClinVar submitters (evaluation after 2014), including two expert panels, have cited the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This variant has been reported in healthy controls and in individuals affected with breast or ovarian cancer in the published literature (PMID: 30652428 (2019), 30287823 (2018), 29907814 (2018), 29383094 (2017), 28993434 (2018)). Additionally, functional studies indicate that this variant interferes with normal BRCA2 mRNA splicing (PMID: 28339459 (2017), 22505045 (2012), 18424508 (2008)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is disease causing and damaging. Variant is located in potentially critical domain of the protein. Therefore, the variant is classified as pathogenic.

The c.8023A>G variant (also known as p.I2675V), located in coding exon 17 of the BRCA2 gene, results from an A to G substitution at nucleotide position 8023. The isoleucine at codon 2675 is replaced by valine, an amino acid with highly similar properties. RNA studies have shown that this alteration creates a new donor site that results in an abnormal transcript with an in-frame loss of 309 nucleotides (Ambry internal data; Bonnet C et al. J Med Genet. 2008 Jul;45(7):438-46; Fraile-Bethencourt E et al. PLoS Genet. 2017 Mar;13:e1006691). In addition, this alteration has been reported in multiple individuals with personal and/or family history consistent with Hereditary Breast and Ovarian Cancer (HBOC) syndrome (Blay P et al. BMC Cancer. 2013 May;13:243; Fernandes GC et al. Oncotarget. 2016 Dec;7:80465-80481; Hirotsu Y et al. Mol Genet Genomic Med. 2015 Mar;3:121-9; Hirotsu Y et al. Oncotarget. 2017 Dec;8:114463-114473; Wen WX et al. J. Med. Genet. 2018 02;55:97-103; Liu Y et al. Mol Genet Genomic Med. 2019 03;7:e493; Tsaousis GN et al. BMC Cancer. 2019 Jun;19:535). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will result in the creation or strengthening of a novel splice donor site. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2675 of the BRCA2 protein (p.Ile2675Val). RNA analysis indicates that this missense change induces altered splicing and likely results in the loss of 103 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs397507954, gnomAD 0.006%). This missense change has been observed in individual(s) with clinical features of hereditary breast and ovarian cancer syndrome (PMID: 18424508, 23683081, 24249303, 25802882, 26757417, 27157322, 27741520). ClinVar contains an entry for this variant (Variation ID: 52475). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt BRCA2 protein function with a negative predictive value of 95%. Studies have shown that this missense change results in the activation of a cryptic splice site in exon 18 (PMID: 18424508, 22505045, 27157322, 28339459, 31191615; internal data). This variant disrupts a region of the BRCA2 protein in which other variant(s) (p.Asp2723His) have been determined to be pathogenic (PMID: 15290653, 15695382, 16489001, 18607349, 23108138, 25146914). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.