Is BRCA2 p.Val300= (c.900A>G) pathogenic?

BRCA2 p.Val300= (c.900A>G) is classified Likely benign in BRCA2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-07-19). Very rare (popmax 0.0035%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Val300= (c.900A>G)?

BRCA2 p.Val300= (c.900A>G) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome (ClinVar).

How common is BRCA2 p.Val300= (c.900A>G) in the general population?

BRCA2 p.Val300= (c.900A>G) is very rare (popmax 0.0035%, amr) (gnomAD).

BRCA2 p.Val300=

c.900A>G · rs1185922157 · VCV1595500

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0035%, amr)

Conditions

hereditary neoplastic syndrome

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 0.64	GERP -1.9, phastCons 0.006
Overall
CADD	1.417	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0035% Admixed American · 2/57,128 alleles

Filtering AF 0.000581% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000217%

Overall 0.000125% 2/1,594,776 alleles · very rare exomes 2/1,442,410 · genomes 0/152,366 · joint denominator

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.Val300=
Coding: c.900A>G
MANE Select: NM_000059
dbSNP: rs1185922157
Type: single nucleotide variant
Location: chr13:32332378 (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

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

Also linked: hereditary breast ovarian cancer syndrome

Similar variants

BRCA2 p.Val300Ala Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Val300Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Val300Ile Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Val300Leu Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Val300_Asp301insTer Pathogenic ★★ same residue
BRCA2 p.Val300fs Pathogenic ★★ same residue
BRCA2 c.316+1G>T Pathogenic ★★★ same condition
BRCA2 c.316+2T>C 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-val300 (accessed [today's date]).

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