BAP1 p.Ser460fs
c.1378_1379del · VCV3662501
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
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 13 of 17 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -4.2 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- BAP1
- Protein
- p.Ser460fs
- Coding
- c.1378_1379del
- MANE Select
- NM_004656
- Type
- Microsatellite
- Location
- chr3:52403766 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.87 · 4 PDB
- Residue 460
- a UniProt-annotated variant site (in tpds1)
Disease context
BAP1-related tumor predisposition syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor BAP1-related tumor predisposition syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adult
Similar variants
- BAP1 p.Ser460Ter Pathogenic ★★ same residue
- BAP1 p.Ser460= Benign/Likely benign ★★ same residue
- BAP1 p.Ser460Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- BAP1 p.Gln267fs Pathogenic ★★ same condition
- BAP1 p.Glu611fs Pathogenic ★★ same condition
- BAP1 p.His481fs Pathogenic ★★ same condition
- BAP1 p.Ser492fs Pathogenic ★★ same condition
- BAP1 p.Val639fs 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-ser460fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown