EEF1A2 p.Arg423=
c.1269C>T · rs900643414 · VCV589916
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00744%, afr)
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 2 | GERP -3.6, phastCons 1 |
| Overall | ||
| CADD | 11.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00744%
African / African-American · 5/67,212 alleles
Filtering AF
0.00287%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00188%
Overall
0.000413%
6/1,453,814 alleles · very rare
exomes 1/1,302,388 · genomes 5/151,426 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00744% | 13,442 |
| European (non-Finnish) | 9.05e-05% | 1,104,657 |
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.Arg423=
- Coding
- c.1269C>T
- MANE Select
- NM_001958
- dbSNP
- rs900643414
- Type
- single nucleotide variant
- Location
- chr20:63488421 (GRCh38)
- Gene constraint
- LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 88.70 · 2 PDB
- Residue 423
- a β-strand
Similar variants
- EEF1A2 p.Arg423Cys Pathogenic/Likely pathogenic ★★ same residue
- EEF1A2 p.Arg423Gln Uncertain significance ★ same residue
- EEF1A2 p.Arg266Trp 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
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-arg423 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown