BAP1 p.Gly614=
c.1842G>A · rs781269263 · VCV417286
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
2
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.41 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.28 | gain · loss 0.07 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.19 | GERP -0.29, phastCons 0.97 |
| Overall | ||
| CADD | 13.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,084 alleles
Overall
6.84e-05%
1/1,461,800 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BAP1
- Protein
- p.Gly614=
- Coding
- c.1842G>A
- MANE Select
- NM_007212 · reported on NM_004656
- dbSNP
- rs781269263
- Type
- single nucleotide variant
- Location
- chr3:52403186 (GRCh38)
- Structure
- AlphaFold pLDDT 78.27 · 28 PDB
Similar variants
- BAP1 p.Gly614Arg Uncertain significance ★★ ⚠ same residue
- BAP1 p.Gly614Val Uncertain significance ★ ⚠ same residue
- BAP1 c.1117-1G>A Likely pathogenic ★★ same condition
- BAP1 c.122+1G>A Pathogenic ★★ same condition
- BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same condition
- BAP1 c.122+5G>A Pathogenic/Likely pathogenic ★★ same condition
- BAP1 c.122+5G>C Likely pathogenic ★★ same condition
- BAP1 c.1251-1G>A 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-gly614 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown