BCOR p.Ala385=
c.1155G>A · rs398124311 · VCV95763
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0103%, 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 -4.3 | GERP -2.7 |
| Overall | ||
| CADD | 1.369 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0103%
European (non-Finnish) · 92/895,441 alleles
Filtering AF
0.00853%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00791%
Overall
0.00784%
95/1,211,001 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0103% | 9,733 |
| African / African-American | 0.00348% | 28,757 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,612 |
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.Ala385=
- Coding
- c.1155G>A
- MANE Select
- NM_001123385
- dbSNP
- rs398124311
- Type
- single nucleotide variant
- Location
- chrX:40074191 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
Similar variants
- BCOR p.Ala385Val Likely benign ★ 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
- BCOR p.Ala1307Pro 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-ala385 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown