Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 11 submitters
gnomAD v4.1
Common
common (popmax 98.1%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
2
Inborn genetic diseases
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 0.25 | GERP -3.2, phastCons 0.066 |
| Overall | ||
| CADD | 0.539 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
98.1%
East Asian · 33,069/33,706 alleles
Filtering AF
97.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 96.9%
Overall
88.1%
1,066,183/1,209,667 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 98.1% | 1 |
| Admixed American | 94.5% | 1 |
| Finnishnot grpmax-eligible | 93.8% | 1 |
| African / African-American | 92.3% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 90.1% | 1 |
| Remaining individualsnot grpmax-eligible | 88.1% | 1 |
| European (non-Finnish) | 87.5% | 1 |
| Middle Eastern | 86.2% | 1 |
| Amishnot grpmax-eligible | 82.6% | 1 |
| South Asian | 77.4% | 1 |
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
- BCOR
- Protein
- p.Asp420=
- Coding
- c.1260T>C
- MANE Select
- NM_001123385
- dbSNP
- rs5917933
- Type
- single nucleotide variant
- Location
- chrX:40074086 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
- Residue 420
- the 'disordered' region
Similar variants
- BCOR p.Asp420Glu Uncertain significance ★ ⚠ same residue
- BCOR p.Arg1163Ter Pathogenic ★★ same condition
- BCOR p.Arg1217Ter Pathogenic ★★ same condition
- BCOR p.Arg1514Ter Pathogenic ★★ same condition
- BCOR p.Arg342Ter Pathogenic ★★ same condition
- BCOR p.Arg810Ter Pathogenic ★★ same condition
- BCOR p.Arg976Ter Pathogenic ★★ same condition
- BCOR p.Ala1262Ser Uncertain significance ★★ ⚠ 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/bcor-p-asp420 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown