EEF2 p.Thr582=
c.1746G>A · rs148878859 · VCV447294
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.215%, amr)
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 -20 | GERP -4.8 |
| Overall | ||
| CADD | 0.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.215%
Admixed American · 87/40,542 alleles
Filtering AF
0.178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.165%
Overall
0.0134%
197/1,467,172 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.215% | 466 |
| African / African-American | 0.062% | 1,612 |
| Remaining individualsnot grpmax-eligible | 0.0266% | 3,759 |
| European (non-Finnish) | 0.00445% | 22,491 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00424% | 23,602 |
| South Asian | 0.00143% | 70,170 |
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
- EEF2
- Protein
- p.Thr582=
- Coding
- c.1746G>A
- MANE Select
- NM_001961
- dbSNP
- rs148878859
- Type
- single nucleotide variant
- Location
- chr19:3978140 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.97 · 26 PDB
- Residue 582
- a β-strand
Similar variants
- EEF2 p.Ala237Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala238Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala338Gly Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala624Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala808Val Uncertain significance ★★ ⚠ same type
- EEF2 p.Arg633His Uncertain significance ★★ ⚠ same type
- EEF2 p.Arg647His Uncertain significance ★★ ⚠ same type
- EEF2 p.Arg726Trp Uncertain significance ★★ ⚠ 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/eef2-p-thr582 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown