Is BRCA1 p.Ser1241Phe (c.3722C>T) pathogenic?

BRCA1 p.Ser1241Phe (c.3722C>T) is classified Uncertain significance in BRCA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-21). AlphaMissense: likely benign (0.1316); Absent from gnomAD v4.1; Associated with Fanconi anemia, complementation group S.

What condition is associated with BRCA1 p.Ser1241Phe (c.3722C>T)?

BRCA1 p.Ser1241Phe (c.3722C>T) is associated with Fanconi anemia, complementation group S (ClinVar).

How common is BRCA1 p.Ser1241Phe (c.3722C>T) in the general population?

BRCA1 p.Ser1241Phe (c.3722C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRCA1 p.Ser1241Phe (c.3722C>T)?

AlphaMissense predicts likely benign (score 0.1316) — an in-silico prediction, not a clinical call.

BRCA1 p.Ser1241Phe

c.3722C>T · VCV3778917

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1316 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Fanconi anemia, complementation group S

Computational evidence

Protein change
AlphaMissense	0.1316	likely benign
REVEL	0.393	indeterminate
SaProt	LLR -8.23	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.2	GERP 0.52, phastCons 0.85
Regional constraint	o/e 0.91	unconstrained · MANE · 78 kb · p 4.8e-05 · regional, not allelic
Overall
CADD	12.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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.Ser1241Phe
Coding: c.3722C>T
MANE Select: NM_007294
Type: single nucleotide variant
Location: chr17:43091809 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB
Residue 1241: a UniProt-annotated variant site (in fancs)

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

Similar variants

BRCA1 p.Ser1241Pro Uncertain significance ★★ ⚠ same residue
BRCA1 p.Ser1241Tyr Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Ser1241Cys Likely benign ★ same residue
BRCA1 c.135-1G>T Pathogenic ★★★ same condition
BRCA1 c.212+1G>A Pathogenic ★★★ same condition
BRCA1 c.213-12A>G Pathogenic ★★★ same condition
BRCA1 c.4675+1G>A Pathogenic ★★★ same condition
BRCA1 c.5074+1G>A 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-ser1241phe (accessed [today's date]).

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