EEF1D p.Pro98Leu
c.293C>T · VCV4246739
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.011 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -3 |
| Regional constraint | o/e 1.01 | unconstrained · MANE · 10 kb · p 0.79 · regional, not allelic |
| Overall | ||
| CADD | 0.009 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
African / African-American · 1/73,456 alleles
Overall
0.000127%
2/1,577,574 alleles · very rare
exomes 1/1,425,326 · genomes 1/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00136% | 73,456 |
| European (non-Finnish) | 8.6e-05% | 1,163,021 |
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.Pro98Leu
- Coding
- c.293C>T
- MANE Select
- NM_001130053
- Type
- single nucleotide variant
- Location
- chr8:143589789 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 4 PDB
- Residue 98
- the 'leucine-zipper' region
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-pro98leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown