BAP1 p.Glu454fs
c.1359dup · rs1351986946 · VCV2008572
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 2.482e-06)
Conditions
2
hereditary neoplastic 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 7.7 | GERP 2.1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
0.000248%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- BAP1
- Protein
- p.Glu454fs
- Coding
- c.1359dup
- MANE Select
- NM_004656
- dbSNP
- rs1351986946
- Type
- Duplication
- Location
- chr3:52403785 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.87 · 4 PDB
- Residue 454
- a UniProt-annotated variant site (in tpds1)
Similar variants
- BAP1 p.Glu454Val Uncertain significance ★★ ⚠ same residue
- BAP1 p.Glu454= Benign/Likely benign ★★ same residue
- BAP1 p.Arg146fs Pathogenic ★★ same condition
- BAP1 p.Asn504fs Pathogenic ★★ same condition
- BAP1 p.Cys320fs Pathogenic ★★ same condition
- BAP1 p.Gln253fs Pathogenic ★★ same condition
- BAP1 p.Gln280fs Pathogenic ★★ same condition
- BAP1 p.Glu198fs Pathogenic/Likely 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-glu454fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown