BCOR p.Ser1278=
c.3834T>C · rs771979613 · VCV2877194
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0239%, amr)
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 0.65 | GERP -2.9, phastCons 0.33 |
| Overall | ||
| CADD | 3.173 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0239%
Admixed American · 11/46,071 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0103%
Overall
0.001%
11/1,096,743 alleles · ultra-rare
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.Ser1278=
- Coding
- c.3834T>C
- MANE Select
- NM_001123385
- dbSNP
- rs771979613
- Type
- single nucleotide variant
- Location
- chrX:40063621 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
- Residue 1278
- the 'disordered' region
Similar variants
- BCOR p.Ser1278Asn 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
- 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-ser1278 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown