BCOR p.Pro1608=
c.4824A>C · rs760093247 · VCV465161
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0592%, eas)
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 -1.9 | GERP -3.5 |
| Overall | ||
| CADD | 1.556 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0592%
East Asian · 20/33,798 alleles
Filtering AF
0.0391%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0328%
Overall
0.00174%
21/1,209,200 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0592% | 1,690 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,589 |
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.Pro1608=
- Coding
- c.4824A>C
- MANE Select
- NM_001123385
- dbSNP
- rs760093247
- Type
- single nucleotide variant
- Location
- chrX:40054038 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
Similar variants
- BCOR p.Pro1608Thr 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-pro1608 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown