GLE1 p.Pro2=
c.6G>T · rs1846592832 · VCV1574794
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 0.005 | GERP -1.6, phastCons 0.76 |
| Overall | ||
| CADD | 9.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,856 alleles
Overall
0.000186%
3/1,608,890 alleles · very rare
exomes 3/1,456,546 · genomes 0/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,856 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,316 |
| African / African-American | 0.00133% | 74,946 |
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.Pro2=
- Coding
- c.6G>T
- MANE Select
- NM_001003722
- dbSNP
- rs1846592832
- Type
- single nucleotide variant
- Location
- chr9:128504811 (GRCh38)
- Gene constraint
- LOEUF 1.103 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.55 · 3 PDB
- Residue 2
- the 'interaction with nup155' region
Similar variants
- GLE1 p.Pro2Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-pro2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown