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BRCA1 encodes a large nuclear protein that helps maintain genomic stability by coordinating the repair of DNA double-strand breaks through homologous recombination, and it also regulates transcription and the cell cycle. It acts as a tumor suppressor, working with proteins such as RAD51, BRCA2, BARD1, and PALB2 to preserve genome integrity. Inherited alterations in BRCA1 cause hereditary breast and ovarian cancer syndrome, with elevated risks of breast, ovarian, prostate, and pancreatic cancers, and biallelic loss underlies a rare form of Fanconi anemia. Because BRCA1-driven tumors rely on impaired DNA repair, they are treatable with PARP inhibitors.
This variant
BRCA1 is a tumor suppressor essential for DNA double-strand break repair, and loss-of-function variants are the established mechanism behind hereditary breast and ovarian cancer risk. This variant creates a premature stop codon predicted to eliminate functional protein through nonsense-mediated decay, consistent with that established disease mechanism, and its complete absence from population databases further supports pathogenic potential, together supporting a Likely Pathogenic classification.
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.1387A>T
GRCh38
chr17:43094144 T>A
GRCh37
chr17:41246161 T>A
Likely Pathogenic from two applicable criteria: PVS1 (Very Strong, predicted nonsense-mediated decay) and PM2 (Supporting, absent from population databases).
Classification rationale
PVS1PM2Likely Pathogenic
BRCA1 c.1387A>Tnonsense · exon 10
PVS1 (Very Strong): nonsense change p.(Lys463Ter) predicted to trigger nonsense-mediated decay. PM2 (Supporting): absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases. Overall: Likely Pathogenic, based on combining one Very Strong and one Supporting criterion per ENIGMA BRCA1/BRCA2 rules.
PVS1 + PM2→Likely Pathogenic
LYFE Sciences is an AI system, and it can make mistakes. Criteria
may be applied incorrectly, sources may be misread, and a confident-looking
classification can still be wrong. Double-check every criterion and
its underlying evidence before relying on any call.
Gene diagram
· NM_007294.4 · variants mapped to exon structure
BRCA1NM_007294.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in BRCA1—click a row to locate it on the plot · use the link column to open its page
Protein
Location
Classification
Link
Applied criteria · 2 applied · 14 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
✓
PVS1very strongPathogenic
Met (Very Strong): this nonsense change creates a premature stop, p.(Lys463Ter), predicted to trigger nonsense-mediated decay well upstream of the final exon.
case_summary.json cspec block: PVS1 defaultStrength 'Pathogenic Very Strong'; rule text: 'Null variant (nonsense, frameshift, splice site...) in a gene where loss of function (LOF) is a known mechanism of disease. Apply at appropriate strength according to PVS1 flowchart... See Specifications Table 4 and Appendix D for details.'pvs1_gene_context.json: gene=BRCA1, germline_disease_context_found=true, lof_mechanism_supported=true, pvs1_gene_gate='eligible', mechanism_rationale citing official CSPEC/VCEP PVS1 guidance for BRCA1.pvs1_variant_assessment.json: consequence_class='nonsense', variant_bucket='nonsense', suggested_default_strength='PVS1', protein change NP_009225.1:p.(Lys463Ter).
Met (Supporting): the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases.
gnomAD v2.1 (exome, non-cancer subset) search for 17-41246161-T-A returned absent, found=false.gnomAD v4.1 search for chr17-43094144-T-A returned absent, found=false.gnomAD-Canada v1.0 (HostSeq genomes) API query for 17-43094144-T-A returned absent, found=false.
Triaged references · 8 PMIDs not cited in assessment
11358863 ↗Tumorigenesis in mice carrying a truncating Brca1 mutation.ONCOKB
12483515 ↗The cancer connection: BRCA1 and BRCA2 tumor suppression in mice and humans.ONCOKB
12947386 ↗Roles of BRCA1 and BRCA2 in homologous recombination, DNA replication fidelity and the cellular response to ionizing radiation.ONCOKB
20608970 ↗BRCA1 16 years later: risk-associated BRCA1 mutations and their functional implications.ONCOKB
17392385 ↗American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.CLINVAR
24366376 ↗Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement.CLINVAR