Is BRCA2 p.Glu865fs (c.2592del) pathogenic?

BRCA2 p.Glu865fs (c.2592del) is classified Pathogenic/Likely pathogenic in BRCA2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-02-18). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Glu865fs (c.2592del)?

BRCA2 p.Glu865fs (c.2592del) is associated with hereditary neoplastic syndrome, breast-ovarian cancer, familial, susceptibility to, 2 (ClinVar).

How common is BRCA2 p.Glu865fs (c.2592del) in the general population?

BRCA2 p.Glu865fs (c.2592del) is absent from gnomAD (gnomAD).

BRCA2 p.Glu865fs

c.2592del · rs2137487979 · VCV1339261

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 11 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1	GERP 1.5

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BRCA2
Protein: p.Glu865fs
Coding: c.2592del
MANE Select: NM_000059
dbSNP: rs2137487979
Type: Deletion
Location: chr13:32336946 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 865: the 'interaction with npm1' region

Full BRCA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: breast-ovarian cancer, familial, susceptibility to, 2

Similar variants

BRCA2 p.Glu865Ter Pathogenic ★★★ same residue
BRCA2 p.Glu865Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Glu865Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Glu865Lys Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 c.316+4del Pathogenic ★★★ same condition
BRCA2 c.5217_5224del Pathogenic ★★★ same condition
BRCA2 c.68-?_316+?del Pathogenic ★★★ same condition
BRCA2 c.7008-?_7805+?del Pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/brca2-p-glu865fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown