Is BRCA2 p.Pro3202fs (c.9603del) pathogenic?

BRCA2 p.Pro3202fs (c.9603del) is classified Pathogenic in BRCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-11). Very rare (popmax 8.47e-05%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Pro3202fs (c.9603del)?

BRCA2 p.Pro3202fs (c.9603del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BRCA2 p.Pro3202fs (c.9603del) in the general population?

BRCA2 p.Pro3202fs (c.9603del) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

BRCA2 p.Pro3202fs

c.9603del · rs2548563785 · VCV1767540

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon within the last 50 nt of the penultimate exon (26 of 27, 47 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.6	GERP 0.94, phastCons 0.005

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,179,948 alleles

Overall 6.2e-05% 1/1,614,102 alleles · very rare exomes 1/1,461,750 · genomes 0/152,352 · 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.Pro3202fs
Coding: c.9603del
MANE Select: NM_000059
dbSNP: rs2548563785
Type: Deletion
Location: chr13:32396997 (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

Similar variants

BRCA2 p.Pro3202= Likely benign ★★★ same residue
BRCA2 p.Pro3202Leu Benign/Likely benign ★★ same residue
BRCA2 p.Pro3202Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 c.5217_5224del Pathogenic ★★★ same condition
BRCA2 c.8312del Pathogenic ★★★ same condition
BRCA2 c.8633-24_8634del Pathogenic ★★★ same condition
BRCA2 c.8756del Pathogenic ★★★ same condition
BRCA2 c.9403del 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-pro3202fs (accessed [today's date]).

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