Is BARD1 p.Ser313Pro (c.937T>C) pathogenic?

BARD1 p.Ser313Pro (c.937T>C) is classified Uncertain significance in BARD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-13). AlphaMissense: likely benign (0.0618); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BARD1 p.Ser313Pro (c.937T>C)?

BARD1 p.Ser313Pro (c.937T>C) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BARD1 p.Ser313Pro (c.937T>C) in the general population?

BARD1 p.Ser313Pro (c.937T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BARD1 p.Ser313Pro (c.937T>C)?

AlphaMissense predicts likely benign (score 0.0618) — an in-silico prediction, not a clinical call.

BARD1 p.Ser313Pro

c.937T>C · rs2469506415 · VCV1766748

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0618 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.0618	likely benign
REVEL	0.128	moderately benign-leaning
SaProt	LLR -7.59	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.77	GERP -2.3
Regional constraint	o/e 1.06	unconstrained · MANE · 81 kb · p 0.077 · regional, not allelic
Overall
CADD	10.48	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: BARD1
Protein: p.Ser313Pro
Coding: c.937T>C
MANE Select: NM_000465
dbSNP: rs2469506415
Type: single nucleotide variant
Location: chr2:214780937 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 64.82 · 11 PDB

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

Similar variants

BARD1 p.Ser313Cys Uncertain significance ★★ ⚠ same residue
BARD1 p.Ser313= Benign/Likely benign ★★ same residue
BARD1 p.Ser313Thr Uncertain significance ★ ⚠ same residue
BARD1 p.Ser313Tyr 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-ser313pro (accessed [today's date]).

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