ClinVar Genomic variation as it relates to human health

Variant summary: BRCA2 c.91T>G (p.Trp31Gly) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250830 control chromosomes (gnomAD). c.91T>G has been reported in the literature, primarily as a VUS in settings of multigene panel testing in individuals affected with breast cancer, most with a family history of HBOC-related and/or other cancers (e.g. Ikeda_2001, Chan_2018, Caleca_2018, Shao_2020, El Ansari_2020). These reports do not necessarily provide unequivocal conclusions about association of the variant with breast cancer or HBOC. Several publications report experimental evidence evaluating an impact on protein function. These studies found that the variant impaired the interaction between BRCA2 and PALB2 (Caleca_2018), was unable to rescue the lethal cell phenotype in an mESC functional complementation assay (Thomassen_2022), and support a damaging effect of this variant on homology directed repair (HDR capacity) based on a high throughput cell based viability assay (MANO-B method) to evaluate drug sensitivity of BRCA2 variants treated with PARP inhibitors (olaparib, niraparib, rucaparib and carboplatin) at various concentrations (Ikegami_2020). The following publications have been ascertained in the context of this evaluation (PMID: 30410870, 30093976, 32778078, 11149425, 32444794, 31742824, 35979650). Three submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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. This variant disrupts the p.Trp31 amino acid residue in BRCA2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9537232, 16793542, 18363094, 19609323, 20215541, 21939546, 22194698, 22678057, 24285729). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects BRCA2 function (PMID: 30410870). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BRCA2 protein function. ClinVar contains an entry for this variant (Variation ID: 481540). This missense change has been observed in individual(s) with breast cancer and/or ovarian cancer (PMID: 30093976, 30410870, 31742824). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces tryptophan, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 31 of the BRCA2 protein (p.Trp31Gly).

This missense variant replaces tryptophan with glycine at codon 31 of the BRCA2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown that this variant has poor complementation in Brca2-deficient mouse embryonic stem cells and demonstrates sensitivity to PARP inhibitors (PMID: 32444794, 35979650). This variant has been reported in individuals affected with early-onset breast cancer and ovarian cancer (PMID: 30093976, 30410870, 32778078). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same codon, c.91T>C (p.Trp31Arg) and c.92G>C (p.Trp31Ser), are considered to be pathogenic (ClinVar Variation ID: 52775, 2098802), suggesting that Trp at this position is important for BRCA2 protein function. 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.W31G variant (also known as c.91T>G), located in coding exon 2 of the BRCA2 gene, results from a T to G substitution at nucleotide position 91. The tryptophan at codon 31 is replaced by glycine, an amino acid with highly dissimilar properties. This variant has been reported in multiple breast cancer families in the literature (Chan GHJ et al. Oncotarget, 2018 Jul;9:30649-30660; Caleca L et al. Front Oncol, 2018 Oct;8:480; Shao D et al. Cancer Sci., 2020 Feb;111:647-657; El Ansari FZ et al. BMC Cancer, 2020 Aug;20:747). This alteration was also reported to abrogate the BRCA2-PALB2 protein binding based on an in vitro assay specifically designed to test the BRCA2-PALB2 interaction (Caleca L et al. Front Oncol, 2018 Oct;8:480). This alteration was non-functional in a cell-survival-based drug sensitivity assay compared to wildtype (Ikegami M et al. Nat Commun, 2020 May;11:2573). In a mouse embryonic stem cell assay this variant led to poor cell viability and the authors noted that the tryptophan residue at codon 31 may be a critical residue for BRCA2PALB2 interaction (Thomassen M et al. Hum Mutat, 2022 Aug). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Published functional studies demonstrate reduced homology-directed repair activity, sensitivity to PARP inhibitors, disrupted PALB2 binding, and poor cell viability, but retained ability to rescue cell growth (PMID: 30410870, 35979650, 32444794, 37731132); Identified in individuals with breast or ovarian cancer, segregating with disease in one family (PMID: 30410870, 30093976, 32778078); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as 319T>G; This variant is associated with the following publications: (PMID: 30410870, 29884841, 35979650, 9537232, 16793542, 19609323, 18363094, 20215541, 21939546, 22194698, 22678057, 32377563, 24285729, 31586400, 31742824, 30093976, 32778078, 32444794, 37731132)