Genetic Information

Gene & Transcript Details

Gene
BRCA2
Transcript
NM_000059.4 MANE Select
Total Exons
Reference Sequence
NC_000013.10
Alternative Transcripts
IDStatusDetails
NM_000059.4 MANE Select 11954 nt | 200–10456
NM_000059.2 Alternative 11386 nt | 228–10484
NM_000059.3 RefSeq Select 11386 nt | 228–10484

Variant Details

HGVS Notation
NM_000059.4:c.7673_7674del
Protein Change
E2558Vfs*7
Location
Exon 16 (Exon 16 of )
16
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.0 in 100,000
Extremely Rare
ACMG Criteria Applied PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).

ClinVar

Open
Classification
Unknown
0 publications
Clinical Statement

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COSMIC Somatic Evidence

Open
COSMIC ID
Recurrence
0 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
COSMIC Preview
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Functional Impact & Domains

Functional Domain

Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene BRCA2.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: BRCA2E2558Vfs*7BRCA2E2558Vfs*7SomaticNCBI Gene:675|Show additional gene information Variant OverviewBRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.The BRCA2 E2558Vfs*7 is a truncating mutation in a tumor suppressor gene, and therefore is likely oncogenic.Hide mutation effect description The mutation effect description for truncating mutations in BRCA2 is: Truncating mutations of BRCA2 can produce several forms of C-terminally truncated BRCA2 proteins. Protein domains that are deleted in BRCA2 truncating mutations include the C-terminal DNA binding domain, the nuclear localization signal and the CDK2 phosphorylation site, the latter which binds RAD51 (PMID: 20878484, 24312913). Experimental studies have shown that truncating mutations impair nuclear localization of BRCA2, essential for normal BRCA2 function (PMID: 10570174). BRCA2 is essential for maintaining the integrity of homologous recombination during DNA damage response (PMID: 11239455). Inactivating or truncating mutations of this gene are associated with a significant increase in lifetime risk for the development of breast, ovarian, prostate or pancreatic cancers (PMID: 22193408). JAX-CKB: No results found

Database Previews
OncoKB
OncoKB Preview
JAX-CKB
JAX-CKB Preview

Click on previews to view full database entries. External databases may require institutional access.

Computational Analysis

Pathogenicity Predictions

SpliceAI
Predictor Consensus
Unknown
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied

SpliceAI Scores

Window: ±500bp
Effect Type Score Position
- Acceptor Loss (AL) 0.05 -52 bp
- Donor Loss (DL) 0.2 35 bp
+ Acceptor Gain (AG) 0.24 5 bp
+ Donor Gain (DG) 0.05 -264 bp
High impact (≥0.5) Medium impact (0.2-0.49) Low impact (<0.2)

VCEP Guidelines

Applied ACMG/AMP Criteria (VCEP Specific)

Filter Criteria:
PVS1

PVS1 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PS3

PS3 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PM2

PM2 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)