Is BRCA1 p.Val1713Glu (c.5138T>A) pathogenic?

BRCA1 p.Val1713Glu (c.5138T>A) is classified Uncertain significance in BRCA1 (ClinVar, No assertion criteria, 2 submitters). AlphaMissense: likely pathogenic (0.9661); Absent from gnomAD v4.1.

How common is BRCA1 p.Val1713Glu (c.5138T>A) in the general population?

BRCA1 p.Val1713Glu (c.5138T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRCA1 p.Val1713Glu (c.5138T>A)?

AlphaMissense predicts likely pathogenic (score 0.9661) — an in-silico prediction, not a clinical call.

BRCA1 p.Val1713Glu

c.5138T>A · rs80357132 · VCV868701

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9661 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9661	likely pathogenic · top 1% in BRCA1
REVEL	0.76	pathogenic-leaning
SaProt	LLR -15.77	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.7, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 78 kb · p 4.8e-05 · regional, not allelic
Overall
CADD	28.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: BRCA1
Protein: p.Val1713Glu
Coding: c.5138T>A
MANE Select: NM_007294
dbSNP: rs80357132
Type: single nucleotide variant
Location: chr17:43063888 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB
Residue 1713: the brct 1 domain; a UniProt-annotated variant site (in fancs); a UniProt-annotated variant site (sequence variant); a β-strand

Full BRCA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BRCA1 p.Val1713Ala Likely pathogenic ★★★ same residue
BRCA1 p.Val1713Leu Likely pathogenic ★ same residue
BRCA1 p.Val1713Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Val1713= Likely benign ★ same residue
BRCA1 p.Val1713fs Pathogenic ★★ same residue
BRCA1 p.Val1713Gly Pathogenic ★ same residue
BRCA1 c.134+3A>T Likely pathogenic ★★★ same type
BRCA1 c.135-1G>T Pathogenic ★★★ same type

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-val1713glu (accessed [today's date]).

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