Is BAP1 p.Glu602del (c.1802AGG[1]) pathogenic?

BAP1 p.Glu602del (c.1802AGG[1]) is classified Conflicting classifications of pathogenicity in BAP1 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-11-05). Very rare (popmax 0.0011%, sas); Associated with BAP1-related tumor predisposition syndrome.

What condition is associated with BAP1 p.Glu602del (c.1802AGG[1])?

BAP1 p.Glu602del (c.1802AGG[1]) is associated with BAP1-related tumor predisposition syndrome, hereditary neoplastic syndrome (ClinVar).

How common is BAP1 p.Glu602del (c.1802AGG[1]) in the general population?

BAP1 p.Glu602del (c.1802AGG[1]) is very rare (popmax 0.0011%, sas) (gnomAD).

How is BAP1-related tumor predisposition syndrome inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

BAP1 p.Glu602del

c.1802AGG[1] · rs2153226476 · VCV1332492

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

BAP1-related tumor predisposition syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.2	GERP 0.55, phastCons 0.003

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,062 alleles

Overall 6.84e-05% 1/1,461,846 alleles · very rare

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: BAP1
Protein: p.Glu602del
Coding: c.1802AGG[1]
MANE Select: NM_007212 · reported on NM_004656
dbSNP: rs2153226476
Type: Microsatellite
Location: chr3:52403221 (GRCh38)
Structure: AlphaFold pLDDT 78.27 · 28 PDB

Full BAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Also linked: hereditary neoplastic syndrome

For BAP1-related tumor predisposition syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

Similar variants

BAP1 p.Glu602Gln Uncertain significance ★★ ⚠ same residue
BAP1 p.Glu602Gly Uncertain significance ★★ ⚠ same residue
BAP1 p.Glu602= Benign/Likely benign ★★ same residue
BAP1 p.Glu602Asp Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Glu602Val Uncertain significance ★ same residue
BAP1 p.Gln267fs Pathogenic ★★ same condition
BAP1 p.Glu611fs Pathogenic ★★ same condition
BAP1 p.His481fs 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-glu602del (accessed [today's date]).

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