Is BAP1 p.Arg264fs (c.788dup) pathogenic?

BAP1 p.Arg264fs (c.788dup) is classified Pathogenic in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-27). Associated with hereditary neoplastic syndrome.

What condition is associated with BAP1 p.Arg264fs (c.788dup)?

BAP1 p.Arg264fs (c.788dup) is associated with hereditary neoplastic syndrome (ClinVar).

BAP1 p.Arg264fs

c.788dup · VCV4867339

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 10 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.56	GERP -3.8, phastCons 0.96

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: BAP1
Protein: p.Arg264fs
Coding: c.788dup
MANE Select: NM_004656
Type: Duplication
Location: chr3:52405907 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB

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.Arg264= Benign/Likely benign ★★ same residue
BAP1 p.Arg264Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Arg146fs Pathogenic ★★ same condition
BAP1 p.Asn504fs Pathogenic ★★ same condition
BAP1 p.Gln253fs Pathogenic ★★ same condition
BAP1 p.Gln280fs Pathogenic ★★ same condition
BAP1 p.Glu198fs Pathogenic/Likely pathogenic ★★ same condition
BAP1 p.Glu454fs Pathogenic/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-arg264fs (accessed [today's date]).

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