Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_007294.4(BRCA1):c.1016del(p.Lys339ArgfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,720 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. K339K) 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
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PVS1 - null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
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PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
PP5
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PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-43094514-CT-C is Pathogenic according to our data. Variant chr17-43094514-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 37386.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43094514-CT-C is described in Lovd as [Pathogenic]. Variant chr17-43094514-CT-C is described in Lovd as [Pathogenic]. Variant chr17-43094514-CT-C is described in Lovd as [Pathogenic]. Variant chr17-43094514-CT-C is described in Lovd as [Pathogenic].
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:6Other:1
not provided, no classification provided
clinical testing
Breast Cancer Information Core (BIC) (BRCA1)
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Pathogenic, no assertion criteria provided
clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
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Pathogenic, no assertion criteria provided
clinical testing
Sharing Clinical Reports Project (SCRP)
May 12, 2009
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Pathogenic, reviewed by expert panel
curation
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Sep 08, 2016
Variant allele predicted to encode a truncated non-functional protein. -
Pathogenic, criteria provided, single submitter
clinical testing
Baylor Genetics
Sep 03, 2022
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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
Michigan Medical Genetics Laboratories, University of Michigan
Nov 03, 2014
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not provided Pathogenic:3
Pathogenic, no assertion criteria provided
clinical testing
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute
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Pathogenic, criteria provided, single submitter
clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano
Nov 28, 2016
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Pathogenic, criteria provided, single submitter
clinical testing
GeneDx
Jul 27, 2018
This deletion of one nucleotide in BRCA1 is denoted c.1016delA at the cDNA level and p.Lys339ArgfsX2 (K339RfsX2) at the protein level. The normal sequence, with the base that is deleted in brackets, is GAAAAAA[delA]GGTA. The deletion causes a frameshift which changes a Lysine to an Arginine at codon 339, and creates a premature stop codon at position 2 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. BRCA1 c.1016delA, previously published as 1129delA and 1135delA using alternate nomenclature, has been reported in several individuals with a personal and/or family history of breast and/or ovarian cancer (Hagervorst 1995, Polreich 2003, Kwong 2009, Fang 2014, Rebbeck 2016). We consider this variant to be pathogenic. -
Hereditary breast ovarian cancer syndrome Pathogenic:3
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
Oct 12, 2023
This sequence change creates a premature translational stop signal (p.Lys339Argfs*2) 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). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with breast and/or ovarian cancer (PMID: 7663517, 15024741, 16287141, 16683254, 22970155, 27157322, 27836010). This variant is also known as 1129delA and 1135delA. ClinVar contains an entry for this variant (Variation ID: 37386). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter
clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Nov 05, 2019
Variant summary: BRCA1 c.1016delA (p.Lys339ArgfsX2) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251174 control chromosomes (gnomAD). c.1016delA has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer (e.g. Rebbeck_2018, Laitman_2019). These data indicate that the variant is very likely to be associated with disease. Five ClinVar submitters including one expert panel (ENIGMA) (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
The c.1016delA pathogenic mutation, located in coding exon 9 of the BRCA1 gene, results from a deletion of one nucleotide at nucleotide position 1016, causing a translational frameshift with a predicted alternate stop codon (p.K339Rfs*2). This alteration, also described as 1135delA and 1129delA, has been detected in multiple, ethnically diverse breast and/or ovarian cancer patients/ families (Hogervorst FB et al. Nat. Genet. 1995 Jun;10(2):208-12; Janatová M et al. Neoplasma 2003; 50(4):246-50; Pohlreich P et al. Med Princ Pract; 2003;12(1):23-9; Azzollini J et al. Eur. J. Intern. Med. 2016 Jul;32:65-71; Carter NJ et al. Gynecol Oncol. 2018 12;151:481-488; Concolino P et al. Int J Mol Sci. 2019 Jul;20:; Laitman Y et al. Hum Mutat. 2019 11;40:e1-e23; Shao D et al. Cancer Sci. 2020 Feb;111:647-657). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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. -
Pathogenic, criteria provided, single submitter
clinical testing
Color Diagnostics, LLC DBA Color Health
Dec 23, 2020
This variant deletes 1 nucleotide in exon 10 of the BRCA1 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with breast and/or ovarian cancer (PMID: 7663517, 9150151, 10874312, 11463009, 16168118, 19353265, 22970155). 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. -
Breast and/or ovarian cancer Pathogenic:1
Pathogenic, no assertion criteria provided
clinical testing
CZECANCA consortium
Jun 11, 2019
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Malignant tumor of breast Uncertain:1
Uncertain significance, no assertion criteria provided
clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System