Is BRCA1 p.Glu1559= (c.4677G>A) pathogenic?

BRCA1 p.Glu1559= (c.4677G>A) is classified Likely benign in BRCA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-16). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA1 p.Glu1559= (c.4677G>A)?

BRCA1 p.Glu1559= (c.4677G>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BRCA1 p.Glu1559= (c.4677G>A) in the general population?

BRCA1 p.Glu1559= (c.4677G>A) is absent from gnomAD v4.1 (gnomAD).

BRCA1 p.Glu1559=

c.4677G>A · VCV3481882

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.86	acceptor gain, 2 bp away · raw score · deltas
Pangolin	Δ0.29	gain · loss 0.01 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP -0.63	GERP -4.6
Overall
CADD	17.09	PHRED · no single calibrated threshold — expert panels disagree

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: BRCA1
Protein: p.Glu1559=
Coding: c.4677G>A
MANE Select: NM_007294
Type: single nucleotide variant
Location: chr17:43071237 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB
Residue 1559: a UniProt-annotated variant site (in fancs)

Full BRCA1 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

BRCA1 p.Glu1559Lys Pathogenic ★★★ ⚠ same residue
BRCA1 p.Glu1559Gln Pathogenic/Likely pathogenic ★★ ⚠ same residue
BRCA1 p.Glu1559Val Uncertain significance ★★ ⚠ same residue
BRCA1 p.Glu1559Ter Pathogenic ★ same residue
BRCA1 p.Glu1559Asp Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Glu1559fs Pathogenic ★★★ same residue
BRCA1 c.134+3A>T Likely pathogenic ★★★ same condition
BRCA1 c.135-1G>T 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-glu1559 (accessed [today's date]).

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