ClinVar Genomic variation as it relates to human health

This variation replaces Arginine with Proline at codon 2336 of the BRCA2 protein. The arginine residue is weakly conserved and is located in a domain of the protein that is not known to be functionally important. There is a moderate physicochemical difference between arginine and proline (Grantham Score 81). This variant also falls at the last nucleotide of exon 13 of the BRCA2 coding sequence, which is part of the consensus splice site for this exon. This variant is not present in population databases (rs28897743, ExAC no frequency). This variant has been reported in individuals with breast and/or ovarian cancer and Fanconi anemia (PMID: 9150172, PMID: 22399190, PMID: 21548014 ). This variant is also known as 7235G>C in the literature. Experimental studies have shown that this missense change causes skipping of exons 12 and 13 (PMID: 22505045). The mutation database ClinVar contains entries for this variant (Variation ID: 52241).

This missense variant replaces arginine with proline at codon 2336 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). This variant also changes the conserved G at the last nucleotide of exon 13 of the BRCA2 gene and is predicted to disrupt RNA splicing. An RNA study has shown that this variant causes skipping of exons 12 and 13, creating a premature translation stop signal in the RNA transcript (PMID: 22505045). This aberrant transcript is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with breast and/or ovarian cancer (PMID: 9150172, 20960228, 21063910, 22399190, 28008555, 32438681). This variant has been identified in 1/247222 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same nucleotide position, c.7007G>A (ClinVar variation ID: 38077), has been shown to produce aberrant RNA transcripts and is considered to be disease-causing. This finding indicates that the reference G nucleotide at the c.7007 position is important for normal RNA splicing. Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 2336 of the BRCA2 protein (p.Arg2336Pro). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs28897743, gnomAD 0.0009%). This missense change has been observed in individual(s) with breast and/or ovarian cancer and Fanconi anemia (PMID: 9150172, 20960228, 21548014, 22399190). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 7235G>C. ClinVar contains an entry for this variant (Variation ID: 52241). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exons 12 and 13 and introduces a premature termination codon (PMID: 22505045). The resulting mRNA is expected to undergo nonsense-mediated decay. This variant disrupts the c.7007G nucleotide in the BRCA2 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 16792514, 20215541, 22505045). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

In silico analysis supports a deleterious effect on splicing; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 7235G>C; This variant is associated with the following publications: (PMID: 29560538, 9150172, 22762150, 26913838, 21523855, 20960228, 26187060, 25256924, 22399190, 21063910, 24312913, 21548014, 28008555, 29086229, 30014164, 21465317, 28973083, 32444794, 30787465, 32341426, 32438681, 34687993, 22505045, 31131967)

Variant summary: The BRCA2 c.7007G>C (p.Arg2336Pro) variant involves the alteration of a conserved nucleotide affecting the last nucleotide of the exon 13. 3/5 in silico tools predict damaging outcome for this variant. 4/5 splice prediction tools predict a significant impact on normal splicing. ESE finder predicts that this variant may generate a novel ESE site. Functional studies showed that the variant causes skipping of exons 12 and 13 (and increase of alternative splicing) (Serova-Sinilnikova, 1997, Houdayer, 2012). This variant is absent in 115936 control chromosomes from ExAC. The variant was found in multiple individuals with a personal/or family history of breast and/or ovarian cancer (Serova-Sinilnikova 1997, Sagi 2010, Adams 2011, Laitman 2011, Laitman 2012, Pritzlaff 2017, Wang 2014). In addition, several clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

The c.7007G>C pathogenic mutation (also known as p.R2336P), located in coding exon 12 of the BRCA2 gene, results from a G to C substitution at nucleotide position 7007. The amino acid change results in arginine to proline at codon 2336, an amino acid with dissimilar properties. This change occurs in the last base pair of coding exon 12, which makes it likely to have some effect on normal mRNA splicing. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Houdayer C et al. Hum. Mutat. 2012 Aug; 33(8):1228-38; Ambry internal data). In addition, this mutation has been reported in numerous individuals with breast and/or ovarian cancer (Serova-Sinilnikova OM et al. Am. J. Hum. Genet. 1997 May; 60(5):1236-9; Laitman Y et al. Breast Cancer Res. Treat. 2011 Jun; 127(2):489-95; Sagi M et al. Fam. Cancer 2011 Mar; 10(1):59-63; Santonocito C et al. Cancers (Basel), 2020 May;12; Tsaousis GN et al. BMC Cancer, 2019 Jun;19:535; Schayek H et al. Breast Cancer Res Treat, 2018 Jul;170:399-404) and has been described as a founder mutation in the Balkan Jewish population (Barnes-Kedar I et al. Breast Cancer Res Treat, 2018 Nov;172:151-157). This mutation has also been detected in conjunction with a nonsense mutation in BRCA2 in an individual with Fanconi anemia (Meng L et al. JAMA Pediatr. 2017 12;171(12):e173438). Of note, this alteration is also designated as 7235G>C in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. However, because this variant is identified in one or more patients with Fanconi Anemia it may be hypomorphic and thus, carriers of this variant and their families may present with reduced risks, and not with the typical clinical characteristics of a high-risk pathogenic BRCA2 alteration. As risk estimates are unknown at this time, clinical correlation is advised.

BRCA2: PM1, PM2, PM5, PS3:Moderate, PS4:Moderate

The p.Arg2336Pro variant has been previously reported in the literature in at least one individual with hereditary breast cancer (Laitman 2011). In addition, this variant has been previously reported in the UMD database (2x as causal), and the BIC database (5x as clinically relevant). The variant is also reported in dbSNP (rs28897743) and may be a low frequency pathogenic variant in one or more populations. The p.Arg2336Pro variant occurs in the last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, in one study, RNA was extracted from lymphoblastoid cell lines and an increase of alternative splicing was observed ('Exons 12 and 13 skipped'), increasing the likelihood this variant has clinical significance (Houdayer 2012). Another variant at the same position (c.7007G>A; p.Arg2336His) has been shown to induce aberrant splicing (Thomassen 2006), also increasing the likelihood a variant at this position is clinically significant. Furthermore, in-silico analysis (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a greater than 10% difference in splicing in 3 of 5 different programs. In summary, based on the above information, this variant is classified as Pathogenic.