Is BAP1 p.Ile675= (c.2025C>A) pathogenic?

BAP1 p.Ile675= (c.2025C>A) is classified Likely benign in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-11). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BAP1 p.Ile675= (c.2025C>A)?

BAP1 p.Ile675= (c.2025C>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BAP1 p.Ile675= (c.2025C>A) in the general population?

BAP1 p.Ile675= (c.2025C>A) is absent from gnomAD v4.1 (gnomAD).

BAP1 p.Ile675=

c.2025C>A · rs1704999360 · VCV1784633

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.063	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.8	GERP -0.16, phastCons 1
Overall
CADD	7.955	PHRED · no single calibrated threshold — expert panels disagree

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: BAP1
Protein: p.Ile675=
Coding: c.2025C>A
MANE Select: NM_004656
dbSNP: rs1704999360
Type: single nucleotide variant
Location: chr3:52402633 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB
Residue 675: an α-helix; the uld domain; a UniProt-annotated variant site (in tpds1); the 'interaction with brca1' region; the 'interaction with yy1' region

Full BAP1 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

BAP1 p.Ile675Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Ile675Ser Uncertain significance ★ ⚠ same residue
BAP1 p.Ile675Val Uncertain significance ★ ⚠ same residue
BAP1 c.1117-1G>A Likely pathogenic ★★ same condition
BAP1 c.122+1G>A Pathogenic ★★ same condition
BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same condition
BAP1 c.1251-1G>A Likely pathogenic ★★ same condition
BAP1 c.1251-2A>G 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/bap1-p-ile675 (accessed [today's date]).

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