BCORL1 p.Pro691=
c.2073C>T · rs368398547 · VCV717643
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.173%, 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 -9.6 | GERP -2.8 |
| Overall | ||
| CADD | 0.052 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.173%
Admixed American · 79/45,689 alleles
Filtering AF
0.142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.131%
Overall
0.00719%
87/1,209,391 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.173% | 578 |
| African / African-American | 0.00527% | 18,988 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,584 |
| South Asian | 0.00176% | 56,741 |
| European (non-Finnish) | 0.000335% | 298,361 |
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.Pro691=
- Coding
- c.2073C>T
- MANE Select
- NM_001379451
- dbSNP
- rs368398547
- Type
- single nucleotide variant
- Location
- chrX:130014845 (GRCh38)
- Structure
- AlphaFold pLDDT 38.79 · 2 PDB
- Residue 691
- a UniProt-annotated variant site (found in a sterile man with oligoasthenoteratozoospermia; likely pathogenic; loss of nuclear localization; loss of interaction with skp1)
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-pro691 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown