BCORL1 p.Pro353=
c.1059G>A · rs372535982 · VCV731196
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0287%, amr)
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 -7.8 | GERP -3.1 |
| Overall | ||
| CADD | 0.023 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0287%
Admixed American · 11/38,356 alleles
Filtering AF
0.016%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0124%
Overall
0.00206%
24/1,164,819 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0287% | 3,487 |
| European (non-Finnish) | 0.00149% | 67,182 |
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.Pro353=
- Coding
- c.1059G>A
- MANE Select
- NM_001379451
- dbSNP
- rs372535982
- Type
- single nucleotide variant
- Location
- chrX:130013831 (GRCh38)
- Structure
- AlphaFold pLDDT 38.79 · 2 PDB
- Residue 353
- the 'disordered' region
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-pro353 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown