Is BRCA1 p.Cys39Phe (c.116G>T) pathogenic?

BRCA1 p.Cys39Phe (c.116G>T) is classified Pathogenic/Likely pathogenic in BRCA1 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-01-09). AlphaMissense: likely pathogenic (0.9928); Absent from gnomAD v4.1; Associated with Inherited ovarian cancer (without breast cancer).

What condition is associated with BRCA1 p.Cys39Phe (c.116G>T)?

BRCA1 p.Cys39Phe (c.116G>T) is associated with Inherited ovarian cancer (without breast cancer), hereditary breast ovarian cancer syndrome, breast-ovarian cancer, familial, susceptibility to, 1 (ClinVar).

How common is BRCA1 p.Cys39Phe (c.116G>T) in the general population?

BRCA1 p.Cys39Phe (c.116G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRCA1 p.Cys39Phe (c.116G>T)?

AlphaMissense predicts likely pathogenic (score 0.9928) — an in-silico prediction, not a clinical call.

BRCA1 p.Cys39Phe

c.116G>T · rs80357498 · VCV37393

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

AlphaMissense

likely pathogenic

0.9928 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inherited ovarian cancer (without breast cancer)

Computational evidence

Protein change
AlphaMissense	0.9928	likely pathogenic ✓ concordant with ClinVar · top 1% in BRCA1
REVEL	0.941	strongly pathogenic-leaning
SaProt	LLR -13.33	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 7.6	GERP 1.8, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 78 kb · p 4.8e-05 · regional, not allelic
Overall
CADD	28.5	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

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.Cys39Phe
Coding: c.116G>T
MANE Select: NM_007294
dbSNP: rs80357498
Type: single nucleotide variant
Location: chr17:43115744 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB

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

Disease context

Inherited ovarian cancer (without breast cancer)

Also linked: hereditary breast ovarian cancer syndrome breast-ovarian cancer, familial, susceptibility to, 1 hereditary neoplastic syndrome

Similar variants

BRCA1 p.Cys39Arg Pathogenic ★★★ same residue
BRCA1 p.Cys39Gly Pathogenic/Likely pathogenic ★★ same residue
BRCA1 p.Cys39Ser Pathogenic/Likely pathogenic ★★ same residue
BRCA1 p.Cys39Ter Pathogenic ★★ same residue
BRCA1 p.Cys39Trp Pathogenic ★★ same residue
BRCA1 p.Cys39Tyr Pathogenic/Likely pathogenic ★★ same residue
BRCA1 p.Cys39_Asp40delinsTer Pathogenic ★★★ same residue
BRCA1 p.Cys39fs Pathogenic ★ same residue

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-cys39phe (accessed [today's date]).

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