EEF1D p.Arg293Trp
c.877C>T · rs369780574 · VCV2362312
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.054%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.163 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -1.2, phastCons 0.26 |
| Regional constraint | o/e 1.01 | unconstrained · MANE · 10 kb · p 0.79 · regional, not allelic |
| Overall | ||
| CADD | 15.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.054%
Admixed American · 31/57,392 alleles
Filtering AF
0.0391%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0339%
Overall
0.00945%
150/1,588,016 alleles · ultra-rare
exomes 114/1,435,664 · genomes 36/152,352 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.054% | 1,851 |
| African / African-American | 0.0268% | 3,731 |
| Remaining individualsnot grpmax-eligible | 0.0196% | 5,101 |
| European (non-Finnish) | 0.00721% | 13,879 |
| South Asian | 0.0034% | 29,429 |
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
- EEF1D
- Protein
- p.Arg293Trp
- Coding
- c.877C>T
- MANE Select
- NM_001130053
- dbSNP
- rs369780574
- Type
- single nucleotide variant
- Location
- chr8:143589205 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 4 PDB
- Residue 293
- a UniProt-annotated variant site (in nedtchal; likely pathogenic)
Similar variants
- EEF1D p.Arg293Leu Uncertain significance ★ same residue
- EEF1D c.1905+1G>A Uncertain significance ★★ same type
- EEF1D p.Arg585Cys Uncertain significance ★★ ⚠ same type
- EEF1D p.Asp100Gly Uncertain significance ★★ same type
- EEF1D p.Asp386Asn Uncertain significance ★★ ⚠ same type
- EEF1D p.Gly351Ala Uncertain significance ★★ same type
- EEF1D p.Pro350Leu Uncertain significance ★★ same type
- EEF1D p.Ser213Asn 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/eef1d-p-arg293trp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown