EEF2 p.Tyr411=
c.1233C>T · rs79533804 · VCV804776
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.29%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.24 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -4.6 |
| Overall | ||
| CADD | 0.938 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.29%
East Asian · 130/44,890 alleles
Filtering AF
0.249%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.234%
Overall
0.0155%
250/1,614,236 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.29% | 345 |
| African / African-American | 0.0599% | 1,668 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.011% | 9,108 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| European (non-Finnish) | 0.00475% | 21,072 |
| Admixed American | 0.00333% | 30,014 |
| Finnishnot grpmax-eligible | 0.00156% | 64,032 |
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.Tyr411=
- Coding
- c.1233C>T
- MANE Select
- NM_001961
- dbSNP
- rs79533804
- Type
- single nucleotide variant
- Location
- chr19:3980627 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.97 · 26 PDB
- Residue 411
- a β-strand
Similar variants
- EEF2 p.Tyr411Phe Uncertain significance ★ same residue
- 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
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-tyr411 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown