EEF1D p.Pro188Arg
c.563C>G · rs138259793 · VCV2220420
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0502%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.081 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP 1.4, phastCons 0.28 |
| Regional constraint | o/e 1.01 | unconstrained · MANE · 10 kb · p 0.79 · regional, not allelic |
| Overall | ||
| CADD | 13.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0502%
African / African-American · 36/71,662 alleles
Filtering AF
0.0373%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0328%
Overall
0.00265%
40/1,510,806 alleles · ultra-rare
exomes 21/1,358,438 · genomes 19/152,368 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0502% | 1,991 |
| Remaining individualsnot grpmax-eligible | 0.00518% | 19,290 |
| European (non-Finnish) | 8.86e-05% | 1,129,038 |
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.Pro188Arg
- Coding
- c.563C>G
- MANE Select
- NM_001130053
- dbSNP
- rs138259793
- Type
- single nucleotide variant
- Location
- chr8:143589519 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 4 PDB
- Residue 188
- a turn; the 'catalytic (gef)' 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-pro188arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown