Is BRCA2 p.Pro3039= (c.9117G>T) pathogenic?

BRCA2 p.Pro3039= (c.9117G>T) is classified Pathogenic/Likely pathogenic in BRCA2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-15). Absent from gnomAD v4.1; Associated with breast-ovarian cancer, familial, susceptibility to, 2.

What condition is associated with BRCA2 p.Pro3039= (c.9117G>T)?

BRCA2 p.Pro3039= (c.9117G>T) is associated with breast-ovarian cancer, familial, susceptibility to, 2, hereditary breast ovarian cancer syndrome (ClinVar).

How common is BRCA2 p.Pro3039= (c.9117G>T) in the general population?

BRCA2 p.Pro3039= (c.9117G>T) is absent from gnomAD v4.1 (gnomAD).

How is Hereditary breast and/or ovarian cancer syndrome inherited?

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

BRCA2 p.Pro3039=

c.9117G>T · rs28897756 · VCV267715

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

breast-ovarian cancer, familial, susceptibility to, 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.92	donor loss at this position · raw score · deltas
Pangolin	Δ0.76	loss · gain 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 3	GERP -0.22, phastCons 1
Overall
CADD	18.96	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BRCA2
Protein: p.Pro3039=
Coding: c.9117G>T
MANE Select: NM_000059
dbSNP: rs28897756
Type: single nucleotide variant
Location: chr13:32379913 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)

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

Disease context

breast-ovarian cancer, familial, susceptibility to, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary breast ovarian cancer syndrome

For Hereditary breast and/or ovarian cancer syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult, Elderly

Similar variants

BRCA2 p.Pro3039Ser Uncertain significance ★★ ⚠ same residue
BRCA2 p.Pro3039Arg Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Pro3039Leu Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Pro3039fs Pathogenic/Likely pathogenic ★★ same residue
BRCA2 p.Pro3039Gln Uncertain significance ★ same residue
BRCA2 c.316+1G>T Pathogenic ★★★ same condition
BRCA2 c.316+2T>C Pathogenic ★★★ same condition
BRCA2 c.316+5G>A 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-pro3039 (accessed [today's date]).

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