GLE1 p.Arg235=
c.705G>A · rs777346999 · VCV1996480
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000124%)
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 0.26 | GERP -2.8, phastCons 0.86 |
| Overall | ||
| CADD | 3.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000124%
Overall
0.000124%
2/1,614,146 alleles · very rare
exomes 2/1,461,870 · genomes 0/152,276 · joint denominator
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.Arg235=
- Coding
- c.705G>A
- MANE Select
- NM_001003722
- dbSNP
- rs777346999
- Type
- single nucleotide variant
- Location
- chr9:128523654 (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-arg235 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown