BCORL1 p.Pro482=
c.1446G>A · rs112032085 · VCV789253
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.52%, afr)
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 0.22 | GERP -3.5, phastCons 0.49 |
| Overall | ||
| CADD | 0.409 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.52%
African / African-American · 1,429/56,686 alleles
Filtering AF
2.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.37%
Overall
0.343%
4,140/1,208,369 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.52% | 40 |
| Ashkenazi Jewishnot grpmax-eligible | 0.545% | 183 |
| Remaining individualsnot grpmax-eligible | 0.399% | 250 |
| Middle Eastern | 0.391% | 256 |
| European (non-Finnish) | 0.247% | 404 |
| Admixed American | 0.241% | 415 |
| Finnishnot grpmax-eligible | 0.0604% | 1,654 |
| South Asian | 0.06% | 1,668 |
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
- BCORL1
- Protein
- p.Pro482=
- Coding
- c.1446G>A
- MANE Select
- NM_001379451
- dbSNP
- rs112032085
- Type
- single nucleotide variant
- Location
- chrX:130014218 (GRCh38)
- Structure
- AlphaFold pLDDT 38.79 · 2 PDB
Similar variants
- BCORL1 p.Ala261Val Uncertain significance ★★ ⚠ same type
- BCORL1 p.Arg1334Gln Uncertain significance ★★ ⚠ same type
- BCORL1 p.Arg1716Gln Uncertain significance ★★ same type
- BCORL1 p.Asp77Val Uncertain significance ★★ ⚠ same type
- BCORL1 p.Gln1076Arg Uncertain significance ★★ ⚠ same type
- BCORL1 p.Glu1201Gln Uncertain significance ★★ ⚠ same type
- BCORL1 p.Glu1256Asp Uncertain significance ★★ ⚠ same type
- BCORL1 p.Glu1744Lys 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/bcorl1-p-pro482 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown