Is BRCA2 p.Ser2509fs (c.7525_7526delinsGACT) pathogenic?

BRCA2 p.Ser2509fs (c.75257526delinsGACT) is classified Likely pathogenic in BRCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-28). Absent from gnomAD; Associated with hereditary breast carcinoma.

What condition is associated with BRCA2 p.Ser2509fs (c.7525_7526delinsGACT)?

BRCA2 p.Ser2509fs (c.7525_7526delinsGACT) is associated with hereditary breast carcinoma (ClinVar).

How common is BRCA2 p.Ser2509fs (c.7525_7526delinsGACT) in the general population?

BRCA2 p.Ser2509fs (c.7525_7526delinsGACT) is absent from gnomAD (gnomAD).

How is Hereditary breast cancer inherited?

Typically Autosomal dominant, Multigenic/multifactorial (Orphanet). A genetic counselor can assess individual risk for a family.

BRCA2 p.Ser2509fs

c.7525_7526delinsGACT · rs2548541468 · VCV2680263

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary breast carcinoma

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 15 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.9	GERP 2.3, phastCons 1

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.Ser2509fs
Coding: c.7525_7526delinsGACT
MANE Select: NM_000059
dbSNP: rs2548541468
Type: Indel
Location: chr13:32356517 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 2509: the 'interaction with fancd2' region; the 'interaction with sem1' region

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

Disease context

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

For Hereditary breast cancer (Orphanet):

Inheritance: Autosomal dominant, Multigenic/multifactorial
Onset: Adult, Elderly

Similar variants

BRCA2 c.8954-1_8955delinsAA Pathogenic ★★★ same condition
BRCA2 p.Arg2799fs Pathogenic ★★★ same condition
BRCA2 p.Glu1608fs Pathogenic ★★★ same condition
BRCA2 p.Lys1025_Lys1026delinsAsnTer Pathogenic ★★★ same condition
BRCA2 p.Lys2404fs Pathogenic ★★★ same condition
BRCA2 p.Met3118_Leu3119insTer Pathogenic ★★★ same condition
BRCA2 p.Phe1870Ter Pathogenic ★★★ same condition
BRCA2 p.Ser2509Ter Pathogenic ★★★ same residue

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-ser2509fs (accessed [today's date]).

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