ClinVar Genomic variation as it relates to human health

RAD51C: PVS1, PM2

Variant summary: RAD51C c.905-2A>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. A different RAD51C variant located at the same nucleotide, c.905-2A>G, induced loss of exon 7 in the mature transcript, and introduced a frameshift and a stop codon at position 363 (Coulet_2013). The variant allele was found at a frequency of 1.2e-05 in 251338 control chromosomes. c.905-2A>C has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Han Lin_2016, Norquist_2016, Wang_2018). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (n=1)/likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as likely pathogenic.

Canonical splice site variant demonstrated to result in aberrant splicing in a gene for which loss of function is a known mechanism of disease (Sanoguera-Miralles et al., 2020); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 29566657, 32980694, 29922827, 26824983, 26720728, 28188963, 22725699, 30093976, 31815095, 30875412, 24800917, 33333735, 36243179, 36988593, 21990120, 35014770, 16199547, 33649982, 35740625, 33471991, 20400964, 35070981, 31159747)

This variant causes an A to C nucleotide substitution at the -2 position of intron 6 of the RAD51C gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. RNA studies have shown that this variant causes the skipping of exon 7 (PMID: 33333735) and is expected to result in an absent or disrupted protein product. This variant has been reported in individuals affected with ovarian cancer (PMID: 26720728, 30093976, 30875412, 31815095), breast cancer (PMID: 26824983, 29566657, 33471991; DOI: 10.21203/rs.3.rs-122156/v1), and colorectal cancer (PMID: 33563768, 35014770). In a large international case-control study, this variant was reported in 6/60466 breast cancer cases and 1/53461 controls (OR=5.305, 95%CI 0.639 to 44.07, p-value=0.13; PMID: 33471991). This variant has been identified in 4/282730 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same splice acceptor site, c.905-2A>G, is known to be disease-causing (ClinVar Variation ID: 245991). Loss of RAD51C function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic.

This sequence change affects an acceptor splice site in intron 6 of the RAD51C gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in RAD51C are known to be pathogenic (PMID: 20400964, 21990120, 24800917, 29278735). This variant is present in population databases (rs779582317, gnomAD 0.02%). Disruption of this splice site has been observed in individual(s) with breast cancer (PMID: 26824983). ClinVar contains an entry for this variant (Variation ID: 216132). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the c.905-2A nucleotide in the RAD51C gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 22725699). 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.

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

The c.905-2A>C intronic variant results from an A to C substitution two nucleotides upstream from coding exon 7 in the RAD51C gene. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. This variant has been reported in the literature in individuals suspected to be affected with hereditary breast or ovarian cancer (Lin PH et al. Oncotarget, 2016 Feb;7:8310-20, Norquist BM et al. JAMA Oncol, 2016 Apr;2:482-90, Chan GHJ et al. Oncotarget, 2018 Jul;9:30649-30660, Wang YA et al. BMC Cancer, 2018 03;18:315, Ow SGW et al. PLoS One, 2019 Mar;14:e0213746, Manchana T et al. World J Clin Oncol, 2019 Nov;10:358-368). Another study reported the alteration in 6/60,466 breast cancer cases and in 1/53,461 controls (Dorling et al. N Engl J Med. 2021 02;384:428-439). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site. In concordance, this variant was reported to result in skipping of exon 7 in a mini-gene RT-PCR assay (Sanoguera-Miralles L et al. Cancers (Basel), 2020 Dec;12:). Based on the majority of available evidence to date, this variant is likely to be pathogenic.