Is BRCA2 p.Arg787= (c.2359A>C) pathogenic?

BRCA2 p.Arg787= (c.2359A>C) is classified Likely benign in BRCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-31). Absent from gnomAD v4.1; Associated with BRCA2-related cancer predisposition.

What condition is associated with BRCA2 p.Arg787= (c.2359A>C)?

BRCA2 p.Arg787= (c.2359A>C) is associated with BRCA2-related cancer predisposition (ClinVar).

How common is BRCA2 p.Arg787= (c.2359A>C) in the general population?

BRCA2 p.Arg787= (c.2359A>C) is absent from gnomAD v4.1 (gnomAD).

BRCA2 p.Arg787=

c.2359A>C · VCV3778932

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

BRCA2-related cancer predisposition

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.8	GERP -4.6, phastCons 0.031
Overall
CADD	1.569	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.Arg787=
Coding: c.2359A>C
MANE Select: NM_000059
Type: single nucleotide variant
Location: chr13:32336714 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 787: the 'interaction with npm1' region

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

Disease context

BRCA2-related cancer predisposition — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BRCA2 p.Arg787Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Arg787Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 c.517-2A>G Pathogenic ★★★ same condition
BRCA2 c.631+2T>G Pathogenic ★★★ same condition
BRCA2 c.631+4A>G Likely pathogenic ★★★ same condition
BRCA2 c.632-3C>G Likely pathogenic ★★★ same condition
BRCA2 c.6938-2A>G Pathogenic ★★★ same condition
BRCA2 c.7805+3A>C Likely 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-arg787 (accessed [today's date]).

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