BCOR p.Pro1291=
c.3873G>A · rs774132405 · VCV3068935
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0141%, sas)
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 1.7 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 13.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0141%
South Asian · 7/49,656 alleles
Filtering AF
0.00654%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00465%
Overall
0.00136%
13/954,193 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0141% | 7,094 |
| African / African-American | 0.00231% | 43,262 |
| European (non-Finnish) | 0.000617% | 162,098 |
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.Pro1291=
- Coding
- c.3873G>A
- MANE Select
- NM_001123385
- dbSNP
- rs774132405
- Type
- single nucleotide variant
- Location
- chrX:40063046 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
- Residue 1291
- the 'disordered' region
Similar variants
- BCOR p.Pro1291Leu Uncertain significance ★ ⚠ same residue
- BCOR p.Pro1291Ser Uncertain significance ★ ⚠ 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-pro1291 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown