Is BARD1 p.Arg565Cys (c.1693C>T) pathogenic?

BARD1 p.Arg565Cys (c.1693C>T) is classified Uncertain significance in BARD1 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-03-04). AlphaMissense: likely benign (0.1379); Ultra-rare (popmax 0.0164%, mid); Associated with BARD1-related cancer predisposition.

What condition is associated with BARD1 p.Arg565Cys (c.1693C>T)?

BARD1 p.Arg565Cys (c.1693C>T) is associated with BARD1-related cancer predisposition, hereditary neoplastic syndrome, hereditary breast carcinoma (ClinVar).

How common is BARD1 p.Arg565Cys (c.1693C>T) in the general population?

BARD1 p.Arg565Cys (c.1693C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about BARD1 p.Arg565Cys (c.1693C>T)?

AlphaMissense predicts likely benign (score 0.1379) — an in-silico prediction, not a clinical call.

BARD1 p.Arg565Cys

c.1693C>T · rs587782279 · VCV142170

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

AlphaMissense

likely benign

0.1379 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

BARD1-related cancer predisposition

Computational evidence

Protein change
AlphaMissense	0.1379	likely benign
REVEL	0.471	indeterminate
SaProt	LLR -8.41	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 7.5	GERP 2.1, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 81 kb · p 0.077 · regional, not allelic
Overall
CADD	25.5	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

Grpmax group 0.0164% Middle Eastern · 1/6,082 alleles

Filtering AF 0.00594% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00453%

Overall 0.00229% 37/1,613,798 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,082
South Asian	0.011%	9,108
Admixed American	0.00333%	29,998
East Asian	0.00223%	44,864
European (non-Finnish)	0.00186%	53,633
Remaining individualsnot grpmax-eligible	0.0016%	62,476

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.Arg565Cys
Coding: c.1693C>T
MANE Select: NM_000465
dbSNP: rs587782279
Type: single nucleotide variant
Location: chr2:214745839 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 64.82 · 11 PDB
Residue 565: the brct 1 domain

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

Disease context

Also linked: hereditary neoplastic syndrome hereditary breast carcinoma

Similar variants

BARD1 p.Arg565Leu Uncertain significance ★★ ⚠ same residue
BARD1 p.Arg565= Benign/Likely benign ★★ same residue
BARD1 p.Arg565Gly Uncertain significance ★ ⚠ same residue
BARD1 p.Arg565His Conflicting classifications of pathogenicity ★ ⚠ same residue
BARD1 p.Arg565Ser 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

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-arg565cys (accessed [today's date]).

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