Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_007294.4(BRCA1):c.178C>T(p.Gln60Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. Q60Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
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.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-43106490-G-A is Pathogenic according to our data. Variant chr17-43106490-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 54349.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43106490-G-A is described in Lovd as [Pathogenic]. Variant chr17-43106490-G-A is described in Lovd as [Pathogenic].
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:6Other:1
Pathogenic, reviewed by expert panel
curation
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Apr 22, 2016
Variant allele predicted to encode a truncated non-functional protein. -
Pathogenic, criteria provided, single submitter
clinical testing
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge
Oct 02, 2015
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Pathogenic, criteria provided, single submitter
clinical testing
Department of Molecular Diagnostics, Institute of Oncology Ljubljana
Apr 02, 2020
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Pathogenic, no assertion criteria provided
clinical testing
Breast Cancer Information Core (BIC) (BRCA1)
May 29, 2002
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Pathogenic, no assertion criteria provided
clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center
May 05, 2023
The pathogenic family mutation (p.Gln60Ter) was detected in this specimen. Pathogenic mutations in the BRCA1 gene cause Hereditary Breast/Ovarian Cancer syndrome (HBOC). -
Pathogenic, no assertion criteria provided
clinical testing
Sharing Clinical Reports Project (SCRP)
Dec 29, 2009
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not provided, no classification provided
in vitro
Brotman Baty Institute, University of Washington
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not provided Pathogenic:2
Pathogenic, criteria provided, single submitter
clinical testing
GeneDx
Feb 09, 2024
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 297C>T; This variant is associated with the following publications: (PMID: 20215541, 26295337, 25823446, 29453630, 19941162, 24249303, 9333265, 30702160, 29446198, 30548481, 31825140, 33151324, 25525159, 32741062, 28176296, 30209399) -
Pathogenic, criteria provided, single submitter
clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano
Nov 10, 2015
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Hereditary breast ovarian cancer syndrome Pathogenic:2
Pathogenic, no assertion criteria provided
research
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto
Jan 31, 2014
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Pathogenic, criteria provided, single submitter
clinical testing
Invitae
Jan 08, 2022
This sequence change creates a premature translational stop signal (p.Gln60*) in the BRCA1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BRCA1 are known to be pathogenic (PMID: 20104584). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 54349). This variant is also known as 297C>A. This premature translational stop signal has been observed in individual(s) with breast and/or ovarian cancer (PMID: 9333265). This variant is not present in population databases (gnomAD no frequency). -
The p.Q60* pathogenic mutation (also known as c.178C>T), located in coding exon 3 of the BRCA1 gene, results from a C to T substitution at nucleotide position 178. This changes the amino acid from a glutamine to a stop codon within coding exon 3. This alteration has been identified in multiple families with breast and/or ovarian cancer (Arai M et al. J Hum Genet, 2018 Apr;63:447-457; Bhaskaran SP et al. Int J Cancer, 2019 08;145:962-973; Nakamura S et al. Breast Cancer, 2015 Sep;22:462-8; Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620; Schroeder C et al. Breast Cancer Res Treat, 2010 Jul;122:287-97; Shattuck-Eidens D et al. JAMA, 1997 Oct;278:1242-50; Shi T et al. Int J Cancer, 2017 05;140:2051-2059; Yamauchi H et al. Breast Cancer Res Treat, 2018 Dec;172:679-687; Zhang S et al. Gynecol Oncol, 2011 May;121:353-7). This alteration was also identified in a Chinese individual diagnosed with renal cancer under the age of 45 (Wu J et al. Cancer, 2019 04;125:1060-1069). Additionally, this alteration was found to be deleterious in multiple functional assays (Starita LM et al. Genetics, 2015 Jun;200:413-22; Findlay GM et al. Nature, 2018 10;562:217-222). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -