BCORL1 p.Ala261=
c.783G>A · rs61752973 · VCV784731
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.754%, nfe)
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 -3.7 | GERP -2.8 |
| Overall | ||
| CADD | 0.072 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.754%
European (non-Finnish) · 6,748/894,812 alleles
Filtering AF
0.739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.733%
Overall
0.611%
7,383/1,208,526 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.754% | 133 |
| Middle Eastern | 0.506% | 198 |
| Remaining individualsnot grpmax-eligible | 0.483% | 207 |
| Admixed American | 0.346% | 289 |
| Finnishnot grpmax-eligible | 0.238% | 420 |
| South Asian | 0.0988% | 1,013 |
| African / African-American | 0.0897% | 1,114 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0363% | 2,752 |
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.Ala261=
- Coding
- c.783G>A
- MANE Select
- NM_001379451
- dbSNP
- rs61752973
- Type
- single nucleotide variant
- Location
- chrX:130013555 (GRCh38)
- Structure
- AlphaFold pLDDT 38.79 · 2 PDB
Similar variants
- BCORL1 p.Ala261Val Uncertain significance ★★ ⚠ same residue
- 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-ala261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown