Submissions for variant NM_058216.3(RAD51C):c.404G>A (p.Cys135Tyr)

dbSNP: rs767796996

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000217463	SCV000278700	likely pathogenic	Hereditary cancer-predisposing syndrome	2022-11-04	criteria provided, single submitter	clinical testing	The p.C135Y variant (also known as c.404G>A), located in coding exon 2 of the RAD51C gene, results from a G to A substitution at nucleotide position 404. The amino acid change results in cysteine to tyrosine at codon 135, an amino acid with highly dissimilar properties. However, this change occurs in the last base pair of coding exon 2, which makes it likely to have some effect on normal mRNA splicing. This variant has been reported in multiple individuals diagnosed with breast and/or ovarian cancer (Osorio A et al. Hum. Mol. Genet. 2012 Jul;21(13):2889-98; Sánchez-Bermúdez AI et al. Eur J Med Genet. 2018 Jun;61(6):355-361; 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 will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). RNA analyses on another similar variant at the same nucleotide position, p.C135S (c.404G>C), has shown the introduction of a new premature stop codon into the coding sequence (Neidhardt G et al. Eur. J. Cancer Prev. 2017 Mar;26:165-169, Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Invitae	RCV000458645	SCV000550186	pathogenic	Fanconi anemia complementation group O	2024-01-25	criteria provided, single submitter	clinical testing	This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 135 of the RAD51C protein (p.Cys135Tyr). 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 (rs767796996, gnomAD 0.0009%). This missense change has been observed in individual(s) with breast and/or ovarian cancer (PMID: 22451500, 29409816, 33011440). ClinVar contains an entry for this variant (Variation ID: 234175). 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. Experimental studies have shown that this missense change affects RAD51C function (PMID: 22451500). 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 alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 33011440, 33333735; Invitae). This variant disrupts the c.404G nucleotide in the RAD51C gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 27622768; Invitae). 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.
Mendelics	RCV000709503	SCV000839327	likely pathogenic	Hereditary breast ovarian cancer syndrome	2018-07-02	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000217463	SCV000909441	likely pathogenic	Hereditary cancer-predisposing syndrome	2022-07-06	criteria provided, single submitter	clinical testing	This variant causes a G to A nucleotide substitution at the last nucleotide of exon 2 of the RAD51C gene and replaces cysteine with tyrosine at codon 135 of the RAD51C 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). A functional study has reported that this variant impacts protein function as measured by a cellular assay for RAD51 foci formation in response to DNA damage (PMID: 22451500). Furthermore, RNA studies on patient-derived cellular RNA and in minigene splicing assay have also found that this variant causes the partial retention of the first 27 nucleotides of intron 2, introducing of a premature termination codon (PMID: 33011440, 33333735). The aberrant transcript is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with ovarian cancer in the literature (PMID: 22451500, 29409816, 31125277, 33011440). This variant has been identified in 1/246764 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of RAD51C function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000709503	SCV000920120	likely pathogenic	Hereditary breast ovarian cancer syndrome	2019-11-20	criteria provided, single submitter	clinical testing	Variant Summary: RAD51C c.404G>A (p.Cys135Tyr) results in a non-conservative amino acid change located in the DNA recombination and repair protein RecA-like, ATP-binding domain (IPR020588) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. In addition, the variant also affects a conserved nucleotide located in the last position of exon 2. Several computational tools predict a significant impact on normal splicing: three predict the variant abolishes a 5' splicing donor site, while one predicts the variant weakens a 5' donor site. However, these predictions have yet to be confirmed by functional studies. In an in vitro study, two different nucleotide changes affecting the same position, namely c.404G>C and c.404G>T, have been shown to disrupt RAD51C pre-mRNA processing, resulting in the utilization of a cryptic intronic donor site 27 bp downstream of the canonical splice site (Neidhart_2017). Both these variants were shown to completely abolish proper splicing, causing the inclusion of intronic sequences resulting in a missense substitution immediately followed by a stop codon in both instances. Based on these data, our variant of interest can be predicted to result in a similar outcome. The variant allele was found at a frequency of 4e-06 in 247064 control chromosomes. c.404G>A has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Osorio_2012, Sanchez-Bermudez_2018). These data indicate that the variant may be associated with disease. An in vitro study, examining the effect of this variant at the protein level, using an (intronless) cDNA construct, demonstrated an approximately 50% reduction in RAD51C foci formation (a surrogate measure of homology-directed repair) (Osorio_2012). However, in light of the potential strong spliceogenic effect, this finding might not reflect the overall physiological consequence of the variant in-vivo. Four 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 likely pathogenic citing overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was re-classified as likely pathogenic.
GeneDx	RCV001582758	SCV001812635	likely pathogenic	not provided	2022-12-07	criteria provided, single submitter	clinical testing	Alters the last nucleotide of the exon and is demonstrated to promote the use of a cryptic splice site resulting in multiple transcripts with a protein termination codon (Sanoguera-Miralles et al., 2020); Not observed at a significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect: unable to restore RAD51 foci formation (Osorio et al., 2012); This variant is associated with the following publications: (PMID: 25154786, 22451500, 29409816, 24993905, 29922827, 25470109, 23117857, 28829762, 31125277, 33011440, 14704354, 27622768, 32322110, 33086730, 35039523, 33333735, 34923718, 28888541, 35264596)
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV002467443	SCV002762839	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 3	2022-12-09	criteria provided, single submitter	research	PS3, PS4_STR, PM2_SUP, PM5
Baylor Genetics	RCV002467443	SCV004209775	likely pathogenic	Breast-ovarian cancer, familial, susceptibility to, 3	2023-10-16	criteria provided, single submitter	clinical testing