EEF2 p.Lys439del
c.1312AAG[1] · rs1195137689 · VCV2662760
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 19.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,950 alleles
Overall
0.000657%
1/152,278 alleles · very rare
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.Lys439del
- Coding
- c.1312AAG[1]
- MANE Select
- NM_001961
- dbSNP
- rs1195137689
- Type
- Microsatellite
- Location
- chr19:3980543 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.97 · 26 PDB
- Residue 439
- a modified residue (n6-acetyllysine)
Similar variants
- EEF2 p.Ser113del Uncertain significance ★★ same type
- EEF2 c.219-9_219-6del Uncertain significance ★ same type
- EEF2 p.Val813_Phe814insTer Uncertain significance ★ same type
- EEF2 c.898-20_898-14del Likely benign ★ 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-lys439del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown