EEF1D p.Asp518=
c.1554C>T · rs144710704 · VCV2658901
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0467%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.5 | GERP -3.4 |
| Overall | ||
| CADD | 4.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0467%
African / African-American · 35/74,890 alleles
Filtering AF
0.0345%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0303%
Overall
0.00378%
61/1,613,748 alleles · ultra-rare
exomes 41/1,461,572 · genomes 20/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0467% | 2,140 |
| European (non-Finnish) | 0.00212% | 47,199 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
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.Asp518=
- Coding
- c.1554C>T
- MANE Select
- NM_001130053
- dbSNP
- rs144710704
- Type
- single nucleotide variant
- Location
- chr8:143580662 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 4 PDB
- Residue 518
- a UniProt-annotated variant site (in nedtchal; likely pathogenic)
Similar variants
- 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
- EEF1D p.Thr575Met 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-asp518 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown