BAP1 p.Lys451del
c.1351_1353del · VCV3818738
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
Conditions
2
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 12 | GERP 2.1, phastCons 1 |
Variant & gene context
- Gene
- BAP1
- Protein
- p.Lys451del
- Coding
- c.1351_1353del
- MANE Select
- NM_004656
- Type
- Deletion
- Location
- chr3:52403792 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.87 · 4 PDB
- Residue 451
- a UniProt-annotated variant site (in tpds1)
Disease context
BAP1-related tumor predisposition syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: hereditary neoplastic syndrome
For BAP1-related tumor predisposition syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adult
Similar variants
- BAP1 p.Lys451= Likely benign ★★ same residue
- BAP1 p.Lys451Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
- BAP1 c.123-10_129del Likely pathogenic ★★ same condition
- BAP1 c.1729+1del Pathogenic ★★ same condition
- BAP1 c.1984-3_1999del Likely pathogenic ★★ same condition
- BAP1 c.659+1del Likely pathogenic ★★ same condition
- BAP1 p.Ala138fs Pathogenic ★★ same condition
- BAP1 p.Arg207fs 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-lys451del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown