Is BRCA2 p.Arg2659Thr (c.7976G>C) pathogenic?

BRCA2 p.Arg2659Thr (c.7976G>C) is classified Pathogenic in BRCA2 (ClinVar, Expert panel, 3 submitters; last evaluated 2015-08-10). AlphaMissense: likely pathogenic (0.9904); Absent from gnomAD v4.1; Associated with breast-ovarian cancer, familial, susceptibility to, 2.

How common is BRCA2 p.Arg2659Thr (c.7976G>C) in the general population?

BRCA2 p.Arg2659Thr (c.7976G>C) 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.

What do computational predictors say about BRCA2 p.Arg2659Thr (c.7976G>C)?

AlphaMissense predicts likely pathogenic (score 0.9904) — an in-silico prediction, not a clinical call.

BRCA2 p.Arg2659Thr

Q: What condition is associated with BRCA2 p.Arg2659Thr (c.7976G>C)?

BRCA2 p.Arg2659Thr (c.7976G>C) is associated with breast-ovarian cancer, familial, susceptibility to, 2, hereditary neoplastic syndrome (ClinVar).

c.7976G>C · rs80359027 · VCV52455

Pathogenic Expert panel

Classification

Pathogenic

ClinVar

Review

Expert panel ★★★☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.9904 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, REVEL

Conditions

breast-ovarian cancer, familial, susceptibility to, 2

Computational evidence

Protein change
AlphaMissense	0.9904	likely pathogenic ✓ concordant with ClinVar · top 1% in BRCA2
REVEL	0.837	moderately pathogenic-leaning
⇒ AlphaMissense and REVEL both call this damaging.
Splicing
SpliceAI	Δ0.88	donor loss at this position · raw score · deltas
Pangolin	Δ0.77	loss · gain 0.01 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 47 kb · p 0.059 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Arg2659Thr
Coding: c.7976G>C
MANE Select: NM_000059
dbSNP: rs80359027
Type: single nucleotide variant
Location: chr13:32362693 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 2659: a UniProt-annotated variant site (in bc; uncertain significance); the 'interaction with sem1' region

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 neoplastic syndrome

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

Inheritance: Autosomal dominant
Onset: Adult, Elderly

Similar variants

BRCA2 p.Arg2659Gly Pathogenic ★★★ same residue
BRCA2 p.Arg2659Lys Pathogenic ★★ same residue
BRCA2 p.Arg2659Ser Likely pathogenic ★ same residue
BRCA2 p.Arg2659Ile Uncertain significance ★★ ⚠ same residue
BRCA2 p.Arg2659= 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-arg2659thr (accessed [today's date]).

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