BCOR p.Pro407=
c.1221C>T · rs780952868 · VCV699656
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.172%, 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 -5.1 | GERP -3.2 |
| Overall | ||
| CADD | 0.954 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.172%
East Asian · 58/33,779 alleles
Filtering AF
0.136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.124%
Overall
0.00619%
75/1,211,050 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.172% | 582 |
| South Asian | 0.00704% | 14,211 |
| Remaining individualsnot grpmax-eligible | 0.0063% | 15,874 |
| Admixed American | 0.00217% | 45,997 |
| African / African-American | 0.00173% | 57,686 |
| European (non-Finnish) | 0.000894% | 111,913 |
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.Pro407=
- Coding
- c.1221C>T
- MANE Select
- NM_001123385
- dbSNP
- rs780952868
- Type
- single nucleotide variant
- Location
- chrX:40074125 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
- Residue 407
- the 'disordered' region
Similar variants
- 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
- BCOR p.Ala1262Ser 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/bcor-p-pro407 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown