BAP1 p.Tyr401fs
c.1200_1201dup · VCV4962920
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
BAP1-related disorder
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 6.1 | GERP 0.75, 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.
Variant & gene context
- Gene
- BAP1
- Protein
- p.Tyr401fs
- Coding
- c.1200_1201dup
- MANE Select
- NM_004656
- Type
- Duplication
- Location
- chr3:52404501 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.87 · 4 PDB
- Residue 401
- the 'disordered' region; a UniProt-annotated variant site (in tpds1)
Disease context
BAP1-related disorder
Similar variants
- BAP1 p.Tyr401_Glu405delinsTer Pathogenic ★★ same residue
- BAP1 p.Tyr401Ter Pathogenic ★★ same residue
- BAP1 p.Tyr401Asp Uncertain significance ★★ ⚠ same residue
- BAP1 p.Tyr401Cys Uncertain significance ★★ ⚠ same residue
- BAP1 p.Tyr401= Benign/Likely benign ★★ same residue
- BAP1 p.Tyr401_Asp404del Conflicting classifications of pathogenicity ★ same residue
- BAP1 p.Tyr401_Asp408del Uncertain significance ★ same residue
- BAP1 p.Tyr401Glu Conflicting classifications of pathogenicity ★ same residue
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-tyr401fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown