BCOR p.Ser259=
c.777G>A · rs576246224 · VCV2660317
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00436%, amr)
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 -2.8 |
| Overall | ||
| CADD | 0.019 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00436%
Admixed American · 2/45,889 alleles
Filtering AF
0.00273%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00241%
Overall
0.00331%
40/1,210,079 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00436% | 22,945 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,798 |
| European (non-Finnish) | 0.0038% | 26,322 |
| African / African-American | 0.00348% | 28,745 |
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.Ser259=
- Coding
- c.777G>A
- MANE Select
- NM_001123385
- dbSNP
- rs576246224
- Type
- single nucleotide variant
- Location
- chrX:40074569 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
Similar variants
- BCOR p.Ser259Ter Pathogenic ★ 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
- BCOR p.Arg976Ter 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-ser259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown