BCOR p.Arg1396=
c.4188A>G · rs1340294679 · VCV750256
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000448%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.124 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.25 | GERP -0.49, phastCons 0.99 |
| Overall | ||
| CADD | 5.128 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000448%
European (non-Finnish) · 4/892,319 alleles
Filtering AF
0.000105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.1e-05%
Overall
0.000332%
4/1,204,701 alleles · very rare
exomes 4/1,092,152 · genomes 0/112,549 · joint denominator
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.Arg1396=
- Coding
- c.4188A>G
- MANE Select
- NM_001123385
- dbSNP
- rs1340294679
- Type
- single nucleotide variant
- Location
- chrX:40062379 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
Similar variants
- 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
- BCOR p.Arg976Ter Pathogenic ★★ same type
- BCOR p.Ala1262Ser Uncertain significance ★★ ⚠ 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-arg1396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown