Is BARD1 p.Arg641Ter (c.1921C>T) pathogenic?

BARD1 p.Arg641Ter (c.1921C>T) is classified Pathogenic/Likely pathogenic in BARD1 (ClinVar, Multiple submitters, 21 submitters; last evaluated 2026-01-02). Very rare (popmax 0.00535%, afr); Associated with BARD1-related cancer predisposition.

What condition is associated with BARD1 p.Arg641Ter (c.1921C>T)?

BARD1 p.Arg641Ter (c.1921C>T) is associated with BARD1-related cancer predisposition, gastric cancer, hereditary breast ovarian cancer syndrome (ClinVar).

How common is BARD1 p.Arg641Ter (c.1921C>T) in the general population?

BARD1 p.Arg641Ter (c.1921C>T) is very rare (popmax 0.00535%, afr) (gnomAD).

BARD1 p.Arg641Ter

c.1921C>T · rs587781948 · VCV141702

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 21 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00535%, afr)

Conditions

BARD1-related cancer predisposition

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 10 of 11
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.4	GERP -0.59, phastCons 1
Overall
CADD	46.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00535% African / African-American · 4/74,826 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.00118% 19/1,613,374 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00535%	18,706
Remaining individualsnot grpmax-eligible	0.0016%	62,462
European (non-Finnish)	0.00119%	84,260

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: BARD1
Protein: p.Arg641Ter
Coding: c.1921C>T
MANE Select: NM_000465
dbSNP: rs587781948
Type: single nucleotide variant
Location: chr2:214730491 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 64.82 · 11 PDB
Residue 641: the brct 1 domain; an α-helix

Full BARD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Also linked: gastric cancer hereditary breast ovarian cancer syndrome breast cancer hereditary neoplastic syndrome hereditary breast carcinoma

Similar variants

BARD1 p.Arg641Gly Uncertain significance ★★ ⚠ same residue
BARD1 p.Arg641= Benign/Likely benign ★★ same residue
BARD1 p.Arg641Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
BARD1 p.Arg641Glu Uncertain significance ★ same residue
BARD1 c.1314+1G>A Pathogenic/Likely pathogenic ★★ same condition
BARD1 c.1314+1G>T Likely pathogenic ★★ same condition
BARD1 c.1396-1G>A Likely pathogenic ★★ same condition
BARD1 c.1396-1G>C 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/bard1-p-arg641ter (accessed [today's date]).

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