Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.9%, eas)
Conditions
2
Inborn genetic diseases
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 -11 | GERP -3.8 |
| Overall | ||
| CADD | 6.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.9%
East Asian · 1,299/44,862 alleles
Filtering AF
2.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.71%
Overall
0.0907%
1,462/1,612,538 alleles · low-frequency
exomes 1,357/1,460,206 · genomes 105/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.9% | 35 |
| African / African-American | 0.0933% | 1,072 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| Admixed American | 0.00666% | 15,007 |
| European (non-Finnish) | 0.005% | 19,999 |
| South Asian | 0.00439% | 22,772 |
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
- EEF1A2
- Protein
- p.Ala125=
- Coding
- c.375G>A
- MANE Select
- NM_001958
- dbSNP
- rs2274861
- Type
- single nucleotide variant
- Location
- chr20:63495051 (GRCh38)
- Gene constraint
- LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 88.70 · 2 PDB
- Residue 125
- the tr-type g domain; an α-helix
Similar variants
- EEF1A2 p.Ala125Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
- EEF1A2 p.Arg266Trp Pathogenic/Likely pathogenic ★★ same condition
- EEF1A2 p.Arg423Cys Pathogenic/Likely pathogenic ★★ same condition
- EEF1A2 p.Arg69Cys Pathogenic ★★ same condition
- EEF1A2 p.Asp91Asn Pathogenic ★★ ⚠ same condition
- EEF1A2 p.Asp97Asn Pathogenic/Likely pathogenic ★★ same condition
- EEF1A2 p.Glu122Lys Pathogenic/Likely pathogenic ★★ same condition
- EEF1A2 p.Glu124Lys Pathogenic/Likely pathogenic ★★ same condition
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/eef1a2-p-ala125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown