Is BRCA1 p.Ser1841Arg (c.5521A>C) pathogenic?

BRCA1 p.Ser1841Arg (c.5521A>C) is classified Likely pathogenic in BRCA1 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2025-11-06). AlphaMissense: likely pathogenic (0.9963); Absent from gnomAD v4.1; Associated with Inherited breast cancer and ovarian cancer.

What condition is associated with BRCA1 p.Ser1841Arg (c.5521A>C)?

BRCA1 p.Ser1841Arg (c.5521A>C) is associated with Inherited breast cancer and ovarian cancer, hereditary breast ovarian cancer syndrome, breast-ovarian cancer, familial, susceptibility to, 1 (ClinVar).

How common is BRCA1 p.Ser1841Arg (c.5521A>C) in the general population?

BRCA1 p.Ser1841Arg (c.5521A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRCA1 p.Ser1841Arg (c.5521A>C)?

AlphaMissense predicts likely pathogenic (score 0.9963) — an in-silico prediction, not a clinical call.

BRCA1 p.Ser1841Arg

c.5521A>C · rs80357299 · VCV37681

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

AlphaMissense

likely pathogenic

0.9963 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inherited breast cancer and ovarian cancer

Computational evidence

Protein change
AlphaMissense	0.9963	likely pathogenic ✓ concordant with ClinVar · top 1% in BRCA1
REVEL	0.826	moderately pathogenic-leaning
SaProt	LLR -17.32	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.6, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 78 kb · p 4.8e-05 · regional, not allelic
Overall
CADD	26.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Ser1841Arg
Coding: c.5521A>C
MANE Select: NM_007294
dbSNP: rs80357299
Type: single nucleotide variant
Location: chr17:43045749 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB
Residue 1841: a UniProt-annotated variant site (in fancs); the brct 2 domain; an α-helix

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

Disease context

Inherited breast cancer and ovarian cancer

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

Similar variants

BRCA1 p.Ser1841Asn Likely pathogenic ★★★ same residue
BRCA1 p.Ser1841Thr Uncertain significance ★★★ ⚠ same residue
BRCA1 p.Ser1841= Likely benign ★★★ same residue
BRCA1 p.Ser1841Ile Likely pathogenic ★★ same residue
BRCA1 p.Ser1841Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Ser1841fs Pathogenic ★★★ same residue
BRCA1 p.Ser1841Cys Uncertain significance ★ ⚠ same residue
BRCA1 c.134+3A>T Likely 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-ser1841arg (accessed [today's date]).

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