Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 14%, sas) — 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 0.98 | GERP -3.6, phastCons 1 |
| Overall | ||
| CADD | 14.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
14%
South Asian · 10,866/77,504 alleles
Filtering AF
13.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 13.7%
Overall
1.5%
22,207/1,477,194 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 14% | 7 |
| African / African-American | 13.7% | 7 |
| Remaining individualsnot grpmax-eligible | 2% | 50 |
| Middle Eastern | 1.27% | 79 |
| Admixed American | 1.07% | 94 |
| European (non-Finnish) | 0.0301% | 3,319 |
| East Asian | 0.018% | 5,545 |
| Finnishnot grpmax-eligible | 0.0117% | 8,549 |
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.Glu442=
- Coding
- c.1326G>A
- MANE Select
- NM_001958
- dbSNP
- rs1042796
- Type
- single nucleotide variant
- Location
- chr20:63488364 (GRCh38)
- Gene constraint
- LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 88.70 · 2 PDB
- Residue 442
- 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-glu442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown