rs767796996

chr17-58695189-G-Achr17-58695189-G-Cchr17-58695189-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1_Strong PM2 PP3_Moderate PP5_Very_Strong

The ENST00000421782.3(RAD51C):c.404G>A(p.Trp135Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,398 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: RAD51C ENST00000421782.3 stop_gained
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 8.75

Genes affected

RAD51C (HGNC:9820): (RAD51 paralog C) This gene is a member of the RAD51 family. RAD51 family members are highly similar to bacterial RecA and Saccharomyces cerevisiae Rad51 and are known to be involved in the homologous recombination and repair of DNA. This protein can interact with other RAD51 paralogs and is reported to be important for Holliday junction resolution. Mutations in this gene are associated with Fanconi anemia-like syndrome. This gene is one of four localized to a region of chromosome 17q23 where amplification occurs frequently in breast tumors. Overexpression of the four genes during amplification has been observed and suggests a possible role in tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 8 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 17-58695189-G-A is Pathogenic according to our data. Variant chr17-58695189-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 234175.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-58695189-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAD51C	NM_058216.3	c.404G>A	p.Cys135Tyr	missense_variant, splice_region_variant	2/9	ENST00000337432.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51C	ENST00000337432.9	c.404G>A	p.Cys135Tyr	missense_variant, splice_region_variant	2/9	1	NM_058216.3	P2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000405 AC: 1 AN: 246764 Hom.: 0 AF XY: 0.00000748 AC XY: 1 AN XY: 133752

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000899

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1457398 Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2 AN XY: 724394

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 3 Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 16, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jan 02, 2024	This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 33011440]. -
Pathogenic, criteria provided, single submitter	research	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Dec 09, 2022	PS3, PS4_STR, PM2_SUP, PM5 -

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jul 06, 2022	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 08, 2023	The c.404G>A variant (also known as p.C135Y), 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; Guindalini RSC et al. Sci Rep, 2022 Mar;12:4190). 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. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 20, 2019	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. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Dec 07, 2022

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) -

Fanconi anemia complementation group O Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 25, 2024

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.20
Cadd	Pathogenic	35
Dann	Uncertain	0.99
DEOGEN2	Benign	0.24	T;T;D;T;T
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	1.0	D;D;D;D;D
MetaRNN	Pathogenic	0.89	D;D;D;D;D
MetaSVM	Benign	-0.42	T
MutationTaster	Benign	1.0	D;D;N
PrimateAI	Pathogenic	0.79	T
Sift4G	Uncertain	0.026	D;D;D;D;T
Polyphen		1.0	.;.;D;.;.
Vest4		0.91, 0.93
MutPred		0.73		.;Gain of phosphorylation at C135 (P = 0.0652);Gain of phosphorylation at C135 (P = 0.0652);.;.;
MVP		0.86
MPC		1.1
ClinPred		1.0	D
GERP RS		5.1
Varity_R		0.95
gMVP		0.91

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.85		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.24		Position offset: -22
DS_DL_spliceai		0.85		Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs767796996; hg19: chr17-56772550;