Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_007294.4(BRCA1):āc.212G>Cā(p.Arg71Thr) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R71G) has been classified as Pathogenic.
BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]
Verdict is Pathogenic. Variant got 18 ACMG points.
PM1
In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 10 benign, 17 uncertain in NM_007294.4
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr17-43106457-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 17693.Status of the report is reviewed_by_expert_panel, 3 stars.
PP3
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
Variant 17-43106456-C-G is Pathogenic according to our data. Variant chr17-43106456-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 267512.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43106456-C-G is described in Lovd as [Pathogenic].
The c.212G>C pathogenic mutation (also known as p.R71T), located in coding exon 3 of the BRCA1 gene, results from a G to C substitution at nucleotide position 212. The arginine at codon 71 is replaced by threonine, an amino acid with similar properties. This change occurs in the last base pair of coding exon 3, which makes it likely to have some effect on normal mRNA splicing. This alteration was identified in an individual diagnosed with ovarian cancer (Harter P et al. PLoS ONE, 2017 Oct;12:e0186043) and in a large, worldwide study of BRCA1/2 mutation positive families (Rebbeck TR et al. Hum. Mutat., 2018 05;39:593-620). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data).One functional study found that this nucleotide substitution is non-functional in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature, 2018 10;562:217-222). Another alteration impacting the same donor site (p.R71G, c.211A>G) has been has been shown to have a similar impact on splicing (Ambry internal data; Sanz DJ et al. Clin. Cancer Res. 2010 Mar;16:1957-67; Houdayer C et al. Hum. Mutat. 2012 Aug;33:1228-38).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. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter
clinical testing
Color Diagnostics, LLC DBA Color Health
Sep 23, 2021
This missense variant replaces arginine with threonine at codon 71 of the BRCA1 protein and alters the last nucleotide G in exon 4. The last two nucleotides of exon 4 are both highly conserved (PMID: 15060014). Splice site prediction tools suggest that this variant may impact RNA splicing. RNA studies have reported that disruption of one of the conserved nucleotide, c.211A, resulted in the out-of-frame splicing r.191_212del and the in-frame splicing r.135_212del in variant transcripts that partially deletes the RING domain (PMID: 11385711, 20215541, 23683081). These aberrant spliced transcript are expected to produce an absent or nonfunctional protein product. A functional study has reported that this variant, c.212G>C, impacts BRCA1 function in a haploid human cell proliferation assay (PMID: 30209399). This variant has been reported in an individual affected with ovarian cancer (PMID: 29053726). Similar variants c.211A>G and c.212G>A also have been reported in individuals and families affected with breast or ovarian cancer (PMID: 11385711, 23683081, 25480878, 27081505, 28724667, 29435039) and c.211A>G has been reported to segregate with disease with a likelihood ratio for pathogenicity of 383.2656 (PMID: 31131967). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Hereditary breast ovarian cancer syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter
clinical testing
Invitae
Feb 20, 2022
For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg71 amino acid residue in BRCA1. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Experimental studies have shown that this missense change affects BRCA1 function (PMID: 30209399). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 267512). This variant has not been reported in the literature in individuals affected with BRCA1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with threonine, which is neutral and polar, at codon 71 of the BRCA1 protein (p.Arg71Thr). This variant also falls at the last nucleotide of exon 4, which is part of the consensus splice site for this exon. -
Ovarian neoplasm Pathogenic:1
Pathogenic, no assertion criteria provided
research
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne
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