Is BAP1 p.Asp396fs (c.1185dup) pathogenic?

BAP1 p.Asp396fs (c.1185dup) is classified Pathogenic in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-15). No gnomAD frequency available for this variant; Associated with BAP1-related tumor predisposition syndrome.

What condition is associated with BAP1 p.Asp396fs (c.1185dup)?

BAP1 p.Asp396fs (c.1185dup) is associated with BAP1-related tumor predisposition syndrome (ClinVar).

How common is BAP1 p.Asp396fs (c.1185dup) in the general population?

BAP1 p.Asp396fs (c.1185dup) is no gnomAD frequency available for this variant (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.Asp396fs

c.1185dup · rs1553645136 · VCV412415

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

BAP1-related tumor predisposition 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 12 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Region caveats
Repeat context	tandem	(TCATCC)n simple repeat · ambiguous alignment · confidence, not pathogenicity

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BAP1
Protein: p.Asp396fs
Coding: c.1185dup
MANE Select: NM_004656
dbSNP: rs1553645136
Type: Duplication
Location: chr3:52404517 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB
Residue 396: the 'disordered' region; a UniProt-annotated variant site (in tpds1)

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

Disease context

BAP1-related tumor predisposition syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For BAP1-related tumor predisposition syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

Similar variants

BAP1 p.Arg146fs Pathogenic ★★ same condition
BAP1 p.Asn504fs Pathogenic ★★ same condition
BAP1 p.Cys320fs 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
BAP1 p.Glu566Ter Pathogenic ★★ same condition
BAP1 p.Ile214fs 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-asp396fs (accessed [today's date]).

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