BSX p.Glu223=
c.669G>A · rs761694742 · VCV932662
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0172%, mid)
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 -0.43 | GERP -3.6, phastCons 0.065 |
| Overall | ||
| CADD | 7.624 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0172%
Middle Eastern · 1/5,826 alleles
Overall
0.000206%
3/1,459,402 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0172% | 5,826 |
| Finnishnot grpmax-eligible | 0.00161% | 62,182 |
| European (non-Finnish) | 8.48e-05% | 1,179,844 |
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
- BSX
- Protein
- p.Glu223=
- Coding
- c.669G>A
- MANE Select
- NM_001098169
- dbSNP
- rs761694742
- Type
- single nucleotide variant
- Location
- chr11:122977682 (GRCh38)
- Gene constraint
- LOEUF 1.172 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.92
- Residue 223
- the 'disordered' region
Similar variants
- BSX p.Glu223Gln Uncertain significance ★ ⚠ same residue
- BSX p.His231Gln Benign ★★ same type
- BSX p.Ser150= Benign ★★ same type
- BSX p.Ala66Thr Uncertain significance ★ ⚠ same type
- BSX p.Arg133Leu Uncertain significance ★ ⚠ same type
- BSX p.Arg190Cys Uncertain significance ★ ⚠ same type
- BSX p.Arg48Gln Uncertain significance ★ same type
- BSX p.Asp174Asn 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/bsx-p-glu223 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown