Is BRIP1 p.Pro163Ser (c.487C>T) pathogenic?

BRIP1 p.Pro163Ser (c.487C>T) is classified Conflicting classifications of pathogenicity in BRIP1 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-12-31). AlphaMissense: likely benign (0.0807); Absent from gnomAD v4.1; Associated with Fanconi anemia complementation group J.

What condition is associated with BRIP1 p.Pro163Ser (c.487C>T)?

BRIP1 p.Pro163Ser (c.487C>T) is associated with Fanconi anemia complementation group J, hereditary neoplastic syndrome, hereditary breast carcinoma (ClinVar).

How common is BRIP1 p.Pro163Ser (c.487C>T) in the general population?

BRIP1 p.Pro163Ser (c.487C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRIP1 p.Pro163Ser (c.487C>T)?

AlphaMissense predicts likely benign (score 0.0807) — an in-silico prediction, not a clinical call.

BRIP1 p.Pro163Ser

c.487C>T · rs1064795902 · VCV422627

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0807 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Fanconi anemia complementation group J

Computational evidence

Protein change
AlphaMissense	0.0807	likely benign
REVEL	0.094	moderately benign-leaning
SaProt	LLR -5.14	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 5	GERP 0.63, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 68 kb · p 0.065 · regional, not allelic
Overall
CADD	16.19	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: BRIP1
Protein: p.Pro163Ser
Coding: c.487C>T
MANE Select: NM_032043
dbSNP: rs1064795902
Type: single nucleotide variant
Location: chr17:61849149 (GRCh38)
Gene constraint: LOEUF 0.848 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 64.19 · 6 PDB
Residue 163: the helicase atp-binding domain

Full BRIP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Fanconi anemia complementation group J — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome hereditary breast carcinoma

Similar variants

BRIP1 p.Pro163His Uncertain significance ★★ ⚠ same residue
BRIP1 p.Pro163Leu Uncertain significance ★★ ⚠ same residue
BRIP1 p.Pro163= Benign/Likely benign ★★ same residue
BRIP1 p.Pro163Ala Uncertain significance ★ ⚠ same residue
BRIP1 p.Pro163Thr Uncertain significance ★ ⚠ same residue
BRIP1 p.Pro163_Leu164insTer Pathogenic ★ same residue
BACH1 p.Arg163Lys Likely benign ★ same residue
BRIP1 c.1140+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-pro163ser (accessed [today's date]).

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