BCORL1 p.Pro208=
c.624C>T · VCV3771444
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00888%, eas)
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 -3.9 | GERP -2.8 |
| Overall | ||
| CADD | 0.529 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00888%
East Asian · 3/33,765 alleles
Filtering AF
0.00235%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00125%
Overall
0.00132%
16/1,209,274 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00888% | 11,255 |
| South Asian | 0.00176% | 56,736 |
| African / African-American | 0.00175% | 57,033 |
| European (non-Finnish) | 0.00123% | 81,354 |
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.Pro208=
- Coding
- c.624C>T
- MANE Select
- NM_001379451
- Type
- single nucleotide variant
- Location
- chrX:130013396 (GRCh38)
- Structure
- AlphaFold pLDDT 38.79 · 2 PDB
Similar variants
- BCORL1 p.Pro208Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro208 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown