Is BRIP1 p.Ile952Val (c.2854A>G) pathogenic?

BRIP1 p.Ile952Val (c.2854A>G) is classified Conflicting classifications of pathogenicity in BRIP1 (ClinVar, Conflicting submitters, 15 submitters; last evaluated 2026-05-20). AlphaMissense: likely benign (0.0642); Ultra-rare (popmax 0.0602%, eas); Associated with hereditary neoplastic syndrome.

What condition is associated with BRIP1 p.Ile952Val (c.2854A>G)?

BRIP1 p.Ile952Val (c.2854A>G) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome, ovarian cancer (ClinVar).

How common is BRIP1 p.Ile952Val (c.2854A>G) in the general population?

BRIP1 p.Ile952Val (c.2854A>G) is ultra-rare (popmax 0.0602%, eas) (gnomAD).

What do computational predictors say about BRIP1 p.Ile952Val (c.2854A>G)?

AlphaMissense predicts likely benign (score 0.0642) — an in-silico prediction, not a clinical call.

BRIP1 p.Ile952Val

c.2854A>G · rs200239986 · VCV232950

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 15 submitters

AlphaMissense

likely benign

0.0642 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0602%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.0642	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -6.22	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 -0.001	GERP 1.9
Regional constraint	o/e 0.84	unconstrained · MANE · 110 kb · p 3.3e-06 · regional, not allelic
Overall
CADD	1.797	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 0.0602% East Asian · 27/44,862 alleles

Filtering AF 0.0424% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0365%

Overall 0.00273% 44/1,613,632 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0602%	1,662
European (non-Finnish)	0.00136%	73,738
African / African-American	0.00133%	75,012

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: BRIP1
Protein: p.Ile952Val
Coding: c.2854A>G
MANE Select: NM_032043
dbSNP: rs200239986
Type: single nucleotide variant
Location: chr17:61685887 (GRCh38)
Gene constraint: LOEUF 0.848 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 64.19 · 6 PDB
Residue 952: the 'interaction with brca1' region

Full BRIP1 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 ovarian cancer syndrome ovarian cancer Fanconi anemia complementation group J familial ovarian cancer hereditary breast carcinoma

Similar variants

BRIP1 p.Ile952Ser Uncertain significance ★★ ⚠ same residue
BRIP1 p.Ile952Thr Uncertain significance ⚠ same residue
BRIP1 c.1140+1G>A Likely pathogenic ★★ same condition
BRIP1 c.1141-2A>C Likely pathogenic ★★ same condition
BRIP1 c.1141-2A>G Likely pathogenic ★★ same condition
BRIP1 c.1141-2A>T Likely pathogenic ★★ same condition
BRIP1 c.1340+1G>A Pathogenic/Likely pathogenic ★★ same condition
BRIP1 c.1341-1G>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/brip1-p-ile952val (accessed [today's date]).

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