EEF2 p.Pro514=
c.1542G>A · rs563924657 · VCV718576
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.178%, 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 -4.5 |
| Overall | ||
| CADD | 0.238 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.178%
Admixed American · 107/60,022 alleles
Filtering AF
0.151%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.141%
Overall
0.0144%
232/1,613,792 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.178% | 561 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,929 |
| European (non-Finnish) | 0.00975% | 10,261 |
| South Asian | 0.00329% | 30,363 |
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.Pro514=
- Coding
- c.1542G>A
- MANE Select
- NM_001961
- dbSNP
- rs563924657
- Type
- single nucleotide variant
- Location
- chr19:3979871 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.97 · 26 PDB
- Residue 514
- an α-helix
Similar variants
- EEF2 p.Pro514Leu 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-pro514 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown