Is BARD1 p.Pro464Ser (c.1390C>T) pathogenic?

BARD1 p.Pro464Ser (c.1390C>T) is classified Uncertain significance in BARD1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2024-10-30). AlphaMissense: likely pathogenic (0.9071); Very rare (popmax 0.0011%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with BARD1 p.Pro464Ser (c.1390C>T)?

BARD1 p.Pro464Ser (c.1390C>T) is associated with hereditary neoplastic syndrome, hereditary breast carcinoma (ClinVar).

How common is BARD1 p.Pro464Ser (c.1390C>T) in the general population?

BARD1 p.Pro464Ser (c.1390C>T) is very rare (popmax 0.0011%, sas) (gnomAD).

What do computational predictors say about BARD1 p.Pro464Ser (c.1390C>T)?

AlphaMissense predicts likely pathogenic (score 0.9071) — an in-silico prediction, not a clinical call.

BARD1 p.Pro464Ser

c.1390C>T · rs1553619693 · VCV460704

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely pathogenic

0.9071 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.9071	likely pathogenic · top 6% in BARD1
REVEL	0.758	pathogenic-leaning
SaProt	LLR -9.94	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 81 kb · p 0.077 · regional, not allelic
Overall
CADD	29.0	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 0.0011% South Asian · 1/90,996 alleles

Filtering AF 0.00043% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000313%

Overall 0.000754% 11/1,458,306 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	90,996
European (non-Finnish)	0.00085%	117,685

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.Pro464Ser
Coding: c.1390C>T
MANE Select: NM_000465
dbSNP: rs1553619693
Type: single nucleotide variant
Location: chr2:214769237 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 64.82 · 11 PDB
Residue 464: an α-helix

Full BARD1 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 carcinoma

Similar variants

BARD1 p.Pro464Arg Uncertain significance ★★ ⚠ same residue
BARD1 p.Pro464Leu Uncertain significance ★★ ⚠ same residue
BARD1 p.Pro464= Benign/Likely benign ★★ 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
BARD1 c.1396-1G>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/bard1-p-pro464ser (accessed [today's date]).

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