GLE1 p.Pro58=
c.174C>G · rs772263557 · VCV2146632
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0121%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -2.9 |
| Overall | ||
| CADD | 6.056 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0121%
South Asian · 11/91,006 alleles
Filtering AF
0.00677%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00522%
Overall
0.000807%
13/1,610,764 alleles · ultra-rare
exomes 13/1,458,524 · genomes 0/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0121% | 8,273 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,191 |
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
- GLE1
- Protein
- p.Pro58=
- Coding
- c.174C>G
- MANE Select
- NM_001003722
- dbSNP
- rs772263557
- Type
- single nucleotide variant
- Location
- chr9:128508950 (GRCh38)
- Gene constraint
- LOEUF 1.103 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.55 · 3 PDB
Similar variants
- GLE1 c.1881+1G>T Likely pathogenic ★★ same type
- GLE1 c.1964+2T>C Likely pathogenic ★★ same type
- GLE1 c.2029-1G>A Likely pathogenic ★★ same type
- GLE1 c.433-10A>G Pathogenic ★★ same type
- GLE1 p.Arg133Ter Pathogenic/Likely pathogenic ★★ same type
- GLE1 p.Arg282Ter Pathogenic/Likely pathogenic ★★ same type
- GLE1 p.Arg313Ter Pathogenic/Likely pathogenic ★★ same type
- GLE1 p.Arg569His Pathogenic/Likely pathogenic ★★ 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/gle1-p-pro58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown