Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 43.6%, eas) — too common for a highly-penetrant pathogenic allele
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 -14 | GERP -3.8 |
| Overall | ||
| CADD | 0.415 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
43.6%
East Asian · 19,576/44,860 alleles
Filtering AF
43.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 42.9%
Overall
13%
209,230/1,612,748 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 43.6% | 2 |
| Finnishnot grpmax-eligible | 22% | 5 |
| Remaining individualsnot grpmax-eligible | 13.4% | 7 |
| European (non-Finnish) | 12.8% | 8 |
| Ashkenazi Jewishnot grpmax-eligible | 11.6% | 9 |
| Middle Eastern | 9.86% | 10 |
| Admixed American | 8.29% | 12 |
| South Asian | 5.9% | 17 |
| Amishnot grpmax-eligible | 4.06% | 25 |
| African / African-American | 2.31% | 43 |
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.Pro160=
- Coding
- c.480G>A
- MANE Select
- NM_001958
- dbSNP
- rs2274860
- Type
- single nucleotide variant
- Location
- chr20:63494946 (GRCh38)
- Gene constraint
- LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 88.70 · 2 PDB
- Residue 160
- the tr-type g domain; a β-strand
Similar variants
- 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
- EEF1A2 p.Gly384Arg 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-pro160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown