Is BAP1 p.Asp404Ter (c.1209dup) pathogenic?

BAP1 p.Asp404Ter (c.1209dup) is classified Pathogenic in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-04). No gnomAD frequency available for this variant.

How common is BAP1 p.Asp404Ter (c.1209dup) in the general population?

BAP1 p.Asp404Ter (c.1209dup) is no gnomAD frequency available for this variant (gnomAD).

BAP1 p.Asp404Ter

c.1209dup · rs2153226844 · VCV1697547

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	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 5.2	GERP 1.6, 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.Asp404Ter
Coding: c.1209dup
MANE Select: NM_004656
dbSNP: rs2153226844
Type: Duplication
Location: chr3:52404493 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB
Residue 404: the 'disordered' region; a UniProt-annotated variant site (in tpds1)

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

Similar variants

BAP1 p.Asp404_Glu405insAspGluAspAspTyrGluAspAsp Uncertain significance ★ same residue
BAP1 p.Asp404_Glu405insTyrGluAspAsp Uncertain significance ★ same residue
BAP1 p.Asp404= Benign/Likely benign ★★ same residue
BAP1 p.Asp404Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Asp404Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
BAP1 p.Arg146fs Pathogenic ★★ same type
BAP1 p.Asn504fs Pathogenic ★★ same type
BAP1 p.Cys320fs Pathogenic ★★ same type

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-asp404ter (accessed [today's date]).

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