ClinVar Miner

Submissions for variant NM_007294.4(BRCA1):c.5089T>C (p.Cys1697Arg) (rs80356993)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000077594 SCV001161642 pathogenic Breast-ovarian cancer, familial 1 2019-06-18 reviewed by expert panel curation IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 0.999867
Ambry Genetics RCV000163799 SCV000214380 likely pathogenic Hereditary cancer-predisposing syndrome 2015-09-24 criteria provided, single submitter clinical testing The p.C1697R variant (also known as c.5089T>C), located in coding exon 16 of the BRCA1 gene, results from a T to C substitution at nucleotide position 5089. The cysteine at codon 1697 is replaced by arginine, an amino acid with highly dissimilar properties. This alteration has been identified in several Scandinavian breast/ovarian cancer kindreds and has not been reported in control populations (<span style="background-color:initial">Malander S, Eur. J. Cancer 2004 Feb; 40(3):422-8; Thomassen M, Acta Oncol 2008; 47(4):772-7; <span style="background-color:initial">Bergthorsson JT, J. Med. Genet. 2001 Jun; 38(6):361-8)<span style="background-color:initial">. Structural modeling and functional assays evaluating proteolytic degradation, protein stability, transcriptional activation, peptide binding ability have suggested that this alteration results in reduced or loss of wild type function (<span style="background-color:initial">Vallon-Christersson J, Hum. Mol. Genet. 2001 Feb; 10(4):353-60; <span style="background-color:initial">Williams RS, J. Biol. Chem. 2003 Dec; 278(52):53007-16; <span style="background-color:initial">Glover JN, Fam. Cancer 2006 ; 5(1):89-93). <span style="background-color:initial">Multifactorial and computational likelihood models predict this variant to be deleterious (<span style="background-color:initial">Karchin R, PLoS Comput. Biol. 2007 Feb; 3(2):e26; <span style="background-color:initial">Iversen ES, Cancer Epidemiol. Biomarkers Prev. 2011 Jun; 20(6):1078-88). Of note, this alteration is also designated as 5208T>C in published literature. Internal structural analysis predicts that this substitution will disrupt the structure of BRCA2 such that it will impact the protein-protein interaction interfaces (Ambry internal data; Clapperton JA et al. Nat. Struct. Mol. Biol., 2004 Jun;11:512-8<span style="background-color:initial">). Based on protein sequence alignment, this amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be possibly damaging and deleterious by PolyPhen and SIFT in silico<span style="background-color:initial"> analyses, respectively. <span style="background-color:initial">Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001284299 SCV001470009 likely pathogenic not provided 2019-12-01 criteria provided, single submitter clinical testing Not found in the total gnomAD dataset, and the data is high quality. Found in at least one patient with expected phenotype for this gene. Predicted to have a damaging effect on the protein. Located in potentially critical domain of the protein. Assessment of experimental evidence suggests this variant results in abnormal protein function.
Invitae RCV001378925 SCV001576625 likely pathogenic Hereditary breast and ovarian cancer syndrome 2019-12-03 criteria provided, single submitter clinical testing This sequence change replaces cysteine with arginine at codon 1697 of the BRCA1 protein (p.Cys1697Arg). The cysteine residue is highly conserved and there is a large physicochemical difference between cysteine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in individuals affected with breast and/or ovarian cancer (PMID: 11389159, 11157798, 18465347). This variant is also known as 5208T>C in the literature. ClinVar contains an entry for this variant (Variation ID: 55392). This variant has been reported to affect BRCA1 protein function (PMID: 20516115, 11157798, 11389159, 14534301, 30209399, 28398198). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Sharing Clinical Reports Project (SCRP) RCV000077594 SCV000109397 uncertain significance Breast-ovarian cancer, familial 1 2013-04-19 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA1) RCV000077594 SCV000145307 uncertain significance Breast-ovarian cancer, familial 1 1999-04-12 no assertion criteria provided clinical testing
Brotman Baty Institute,University of Washington RCV000077594 SCV001242097 not provided Breast-ovarian cancer, familial 1 no assertion provided in vitro
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357130 SCV001552490 likely pathogenic Malignant tumor of breast no assertion criteria provided clinical testing The BRCA1 p.Cys1697Arg variant was identified in 9 of 1204 proband chromosomes (frequency 0.007) from Danish and Swedish individuals or families with hereditary breast and/or ovarian cancer, bilateral or multifocal breast cancer, or invasive epithelial ovarian carcinoma, and was not identified in 360 control chromosomes from healthy individuals (Malander_2004_14746861, Thomassen_2008_18465347, Bergthorsson_2001_11389159). It was not identified in the GeneInsight-COGR, COSMIC, MutDB, ARUP Laboratories, or Zhejiang Colon Cancer databases. The variant was identified in dbSNP (ID: rs80356993) as “With Likely pathogenic, Uncertain significance allele”, ClinVar and Clinvitae (1x classified as likely pathogenic by Ambry Genetics; 2x classified as uncertain significance by SCRP and BIC; 1x not classified by Invitae), LOVD 3.0 (10x with multiple functional study citations), UMD-LSDB (predicted to be pathogenic), BIC Database (3 samples recorded with clinical importance classified as unknown) databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). Multiple functional studies have investigated the effect of this variant. Limited proteolysis to determine stability of the protein fold using in vitro transcribed/translated material noted that the C1697R mutant showed a particularly low protein expression level (Lee_2010_20516115). Using yeast and mammalian-based transcription assays this variant displayed loss of transcriptional activity, suggesting that it represents a disease-associated mutation, in agreement with pedigree analysis (Vallon-Christersson_2001_11157798). This study notes that C1697R is a dramatic amino acid substitution, from a non-polar residue capable of forming disulfide linkages to a positively charged residue, located in a critical alpha-helix based on the structure of XRCC1 BRCT, and that this variant was found to segregate with disease in 1 family in the study and 3 other breast cancer patients from another study (Bergthorsson_2001_11389159). In a protease-based assay, substitution of arginine showed increased sensitivity to chymotryptic cleavage at 20°C, suggesting that destabilizing effects, rather than the introduction of a new trypsin cleavage site, are responsible for the protease sensitivity (Williams_2003_14534301). A peptide-binding assay determined that the variant has a severe folding effect (Williams_2004_15133503). In a study which screened DNA using SSCA and PTT, the BRCA1 construct containing Arg1697 was not able to activate transcription in this system, supporting the classification of C1697R as a pathogenic mutation (Bergthorsson_2001_11389159). The p.Cys1697Arg residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.

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