BOK p.Thr103=
c.309C>T · VCV3992378
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0535%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3 |
| Overall | ||
| CADD | 0.423 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0535%
East Asian · 24/44,882 alleles
Filtering AF
0.0368%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0313%
Overall
0.00347%
56/1,612,192 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0535% | 1,870 |
| Middle Eastern | 0.0165% | 6,056 |
| South Asian | 0.011% | 9,106 |
| European (non-Finnish) | 0.00178% | 56,183 |
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
- BOK
- Protein
- p.Thr103=
- Coding
- c.309C>T
- MANE Select
- NM_032515
- Type
- single nucleotide variant
- Location
- chr2:241562436 (GRCh38)
- Gene constraint
- LOEUF 1.824 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.33 · 1 PDB
- Residue 103
- an α-helix
Similar variants
- BOK p.Ala11Val Uncertain significance ★ ⚠ same type
- BOK p.Ala12Gly Uncertain significance ★ ⚠ same type
- BOK p.Ala141Thr Uncertain significance ★ ⚠ same type
- BOK p.Ala148Thr Uncertain significance ★ ⚠ same type
- BOK p.Ala192Val Uncertain significance ★ ⚠ same type
- BOK p.Ala41Thr Uncertain significance ★ ⚠ same type
- BOK p.Ala56Gly Uncertain significance ★ ⚠ same type
- BOK p.Ala57Thr Uncertain significance ★ ⚠ same type
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/bok-p-thr103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown