Is BRCA2 p.Ser758Arg (c.2274T>G) pathogenic?

BRCA2 p.Ser758Arg (c.2274T>G) is classified Conflicting classifications of pathogenicity in BRCA2 (ClinVar, Conflicting submitters, 10 submitters; last evaluated 2026-01-27). AlphaMissense: likely benign (0.2473); Ultra-rare (popmax 0.036%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Ser758Arg (c.2274T>G)?

BRCA2 p.Ser758Arg (c.2274T>G) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome, breast cancer (ClinVar).

How common is BRCA2 p.Ser758Arg (c.2274T>G) in the general population?

BRCA2 p.Ser758Arg (c.2274T>G) is ultra-rare (popmax 0.036%, afr) (gnomAD).

What do computational predictors say about BRCA2 p.Ser758Arg (c.2274T>G)?

AlphaMissense predicts likely benign (score 0.2473) — an in-silico prediction, not a clinical call.

BRCA2 p.Ser758Arg

c.2274T>G · rs142243359 · VCV141084

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 10 submitters

AlphaMissense

likely benign

0.2473 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.036%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.2473	likely benign
REVEL	0.237	benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.31	GERP -4.6
Regional constraint	o/e 1.03	unconstrained · MANE · 47 kb · p 0.059 · regional, not allelic
Overall
CADD	4.822	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.036% African / African-American · 27/74,936 alleles

Filtering AF 0.0254% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0219%

Overall 0.00204% 33/1,613,986 alleles · ultra-rare exomes 13/1,461,790 · genomes 20/152,196 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.036%	2,775
Admixed American	0.01%	9,999

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BRCA2
Protein: p.Ser758Arg
Coding: c.2274T>G
MANE Select: NM_000059
dbSNP: rs142243359
Type: single nucleotide variant
Location: chr13:32336629 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 758: 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: hereditary breast ovarian cancer syndrome breast cancer breast-ovarian cancer, familial, susceptibility to, 2

Similar variants

BRCA2 p.Ser758= Likely benign ★★★ same residue
BRCA2 p.Ser758Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Ser758fs Pathogenic ★★★ 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
BRCA2 c.316+5G>C Pathogenic ★★★ same condition
BRCA2 c.475+1G>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-ser758arg (accessed [today's date]).

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