Is BRCA1 p.Val802fs (c.2405_2406del) pathogenic?

BRCA1 p.Val802fs (c.24052406del) is classified Pathogenic in BRCA1 (ClinVar, Multiple submitters, 13 submitters; last evaluated 2026-03-27). Very rare (popmax 0.00329%, sas); Associated with Fanconi anemia, complementation group S.

What condition is associated with BRCA1 p.Val802fs (c.2405_2406del)?

BRCA1 p.Val802fs (c.2405_2406del) is associated with Fanconi anemia, complementation group S, hereditary breast ovarian cancer syndrome, breast-ovarian cancer, familial, susceptibility to, 1 (ClinVar).

How common is BRCA1 p.Val802fs (c.2405_2406del) in the general population?

BRCA1 p.Val802fs (c.2405_2406del) is very rare (popmax 0.00329%, sas) (gnomAD).

BRCA1 p.Val802fs

c.2405_2406del · rs80357706 · VCV54558

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 13 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00329%, sas)

Conditions

Fanconi anemia, complementation group S

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	predicted	premature termination codon in exon 10 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.22	GERP -3.9

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00329% South Asian · 3/91,050 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.000186% 3/1,613,676 alleles · very rare exomes 3/1,461,388 · genomes 0/152,288 · 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: BRCA1
Protein: p.Val802fs
Coding: c.2405_2406del
MANE Select: NM_007294
dbSNP: rs80357706
Type: Microsatellite
Location: chr17:43093125 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB

Full BRCA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Fanconi anemia, complementation group S — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary breast ovarian cancer syndrome breast-ovarian cancer, familial, susceptibility to, 1 hereditary neoplastic syndrome breast neoplasm

Similar variants

BRCA1 p.Val802= Likely benign ★★ same residue
BRCA1 p.Val802Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Val802Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Val802Met Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Ala1082_Met1083insTer Pathogenic ★★★ same condition
BRCA1 p.Ala92fs Pathogenic ★★★ same condition
BRCA1 p.Arg1583fs Pathogenic ★★★ same condition
BRCA1 p.Arg163Ter 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/brca1-p-val802fs (accessed [today's date]).

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