BCOR p.Leu808=
c.2424T>C · rs142968718 · VCV760313
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.279%, afr)
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 -1.3 | GERP -3.4 |
| Overall | ||
| CADD | 1.054 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.279%
African / African-American · 159/56,965 alleles
Filtering AF
0.244%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.23%
Overall
0.0143%
173/1,209,359 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.279% | 358 |
| Remaining individualsnot grpmax-eligible | 0.0147% | 6,801 |
| Admixed American | 0.0131% | 7,629 |
| European (non-Finnish) | 0.000112% | 894,991 |
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.Leu808=
- Coding
- c.2424T>C
- MANE Select
- NM_001123385
- dbSNP
- rs142968718
- Type
- single nucleotide variant
- Location
- chrX:40072922 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
Similar variants
- BCOR p.Leu808Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
- BCOR p.Leu808His Benign/Likely benign ★★ same residue
- BCOR p.Arg1163Ter Pathogenic ★★ same type
- BCOR p.Arg1164Ter Pathogenic ★★ same type
- BCOR p.Arg1217Ter Pathogenic ★★ same type
- BCOR p.Arg1514Ter Pathogenic ★★ same type
- BCOR p.Arg342Ter Pathogenic ★★ same type
- BCOR p.Arg810Ter Pathogenic ★★ 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/bcor-p-leu808 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown