EEF1D p.Ala35=
c.105G>A · rs777359937 · VCV3053384
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
EEF1D-related disorder
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 -0.48 | GERP -2.6 |
| Overall | ||
| CADD | 6.054 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,078 alleles
Filtering AF
0.0018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00157%
Overall
0.00213%
34/1,599,166 alleles · ultra-rare
exomes 33/1,446,920 · genomes 1/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,078 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,574 |
| European (non-Finnish) | 0.00254% | 39,320 |
| South Asian | 0.0022% | 45,518 |
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.Ala35=
- Coding
- c.105G>A
- MANE Select
- NM_001130053
- dbSNP
- rs777359937
- Type
- single nucleotide variant
- Location
- chr8:143589977 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 4 PDB
Disease context
EEF1D-related disorder
Similar variants
- 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.Ala549Ser Likely benign same condition
- EEF1D p.Ala578= Benign same condition
- EEF1D p.Arg110= Benign same condition
- EEF1D p.Arg336= 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-ala35 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown