EEF1D p.Val584=
c.1752G>C · rs548361410 · VCV3040141
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.905%, sas)
Conditions
1
EEF1D-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.078 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.89 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 15.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.905%
South Asian · 824/91,084 alleles
Filtering AF
0.853%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.833%
Overall
0.0529%
854/1,613,788 alleles · rare
exomes 826/1,461,472 · genomes 28/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.905% | 111 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,976 |
| Middle Eastern | 0.033% | 3,026 |
| East Asian | 0.00223% | 44,884 |
| Admixed American | 0.00167% | 60,006 |
| African / African-American | 0.00133% | 75,040 |
| European (non-Finnish) | 0.000339% | 295,004 |
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.Val584=
- Coding
- c.1752G>C
- MANE Select
- NM_001130053
- dbSNP
- rs548361410
- Type
- single nucleotide variant
- Location
- chr8:143580165 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 4 PDB
- Residue 584
- a UniProt-annotated variant site (in nedtchal; likely pathogenic)
Disease context
EEF1D-related disorder
Similar variants
- EEF1D p.Val584Met Uncertain significance ★ ⚠ same residue
- EEF1D p.Asp386Asn Uncertain significance ★★ ⚠ same condition
- EEF1D p.Arg292Ter Likely pathogenic ★ same condition
- EEF1D p.Gln610Ter Likely pathogenic ★ same condition
- EEF1D c.1288-10T>C Likely benign same condition
- EEF1D p.Ala35= Likely benign same condition
- EEF1D p.Ala549Ser Likely benign same condition
- EEF1D p.Ala578= Benign 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/eef1d-p-val584 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown