BCOR p.Pro838=
c.2514C>A · rs147497014 · VCV166749
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.241%, nfe)
Conditions
1
microphthalmia, syndromic 2
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 4.6 | GERP 0.67, phastCons 1 |
| Overall | ||
| CADD | 2.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.241%
European (non-Finnish) · 2,158/895,136 alleles
Filtering AF
0.233%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.229%
Overall
0.185%
2,241/1,209,738 alleles · rare
exomes 2,155/1,098,075 · genomes 86/111,663 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.241% | 415 |
| Remaining individualsnot grpmax-eligible | 0.113% | 881 |
| African / African-American | 0.0386% | 2,593 |
| Admixed American | 0.00655% | 15,268 |
| Finnishnot grpmax-eligible | 0.00644% | 15,528 |
| East Asian | 0.00296% | 33,781 |
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.Pro838=
- Coding
- c.2514C>A
- MANE Select
- NM_001123385
- dbSNP
- rs147497014
- Type
- single nucleotide variant
- Location
- chrX:40072832 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
- Residue 838
- the 'disordered' region
Similar variants
- BCOR p.Pro838Ser Benign/Likely benign ★★ same residue
- BCOR p.Pro838His 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.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-pro838 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown