Is BRCA1 p.Gln1388Arg (c.4163A>G) pathogenic?

BRCA1 p.Gln1388Arg (c.4163A>G) is classified Uncertain significance in BRCA1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-02). AlphaMissense: likely benign (0.1555); Very rare (popmax 0.000594%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA1 p.Gln1388Arg (c.4163A>G)?

BRCA1 p.Gln1388Arg (c.4163A>G) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome, breast-ovarian cancer, familial, susceptibility to, 1 (ClinVar).

How common is BRCA1 p.Gln1388Arg (c.4163A>G) in the general population?

BRCA1 p.Gln1388Arg (c.4163A>G) is very rare (popmax 0.000594%, nfe) (gnomAD).

What do computational predictors say about BRCA1 p.Gln1388Arg (c.4163A>G)?

AlphaMissense predicts likely benign (score 0.1555) — an in-silico prediction, not a clinical call.

BRCA1 p.Gln1388Arg

c.4163A>G · rs1246721860 · VCV1020675

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1555 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000594%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1555	likely benign
REVEL	0.679	pathogenic-leaning
SaProt	LLR -6.90	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.2, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 78 kb · p 4.8e-05 · regional, not allelic
Overall
CADD	22.4	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

Grpmax group 0.000594% European (non-Finnish) · 7/1,179,168 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.00048% 7/1,459,724 alleles · very rare

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.Gln1388Arg
Coding: c.4163A>G
MANE Select: NM_007294
dbSNP: rs1246721860
Type: single nucleotide variant
Location: chr17:43090966 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB
Residue 1388: 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

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

Similar variants

BRCA1 p.Gln1388Ter Pathogenic ★★★ same residue
BRCA1 p.Gln1388His Uncertain significance ★★ ⚠ same residue
BRCA1 p.Gln1388Lys Uncertain significance ★★ ⚠ same residue
BRCA1 p.Gln1388= Likely benign ★ same residue
BRCA1 p.Gln1388_Ser1389insTer Pathogenic ★★★ same residue
BRCA1 p.Gln1388fs 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-gln1388arg (accessed [today's date]).

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