Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 18%, sas) — too common for a highly-penetrant pathogenic allele
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 1.3 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 11.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
18%
South Asian · 16,393/91,048 alleles
Filtering AF
17.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.7%
Overall
9.33%
150,439/1,612,540 alleles · common
exomes 139,907/1,460,298 · genomes 10,532/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 18% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 9.82% | 10 |
| European (non-Finnish) | 9.77% | 10 |
| Amishnot grpmax-eligible | 9.56% | 10 |
| Middle Eastern | 9.45% | 11 |
| Remaining individualsnot grpmax-eligible | 8.82% | 11 |
| Finnishnot grpmax-eligible | 8.31% | 12 |
| Admixed American | 3.47% | 29 |
| East Asian | 2.52% | 40 |
| African / African-American | 1.71% | 59 |
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
- EEF2
- Protein
- p.Arg150=
- Coding
- c.450C>T
- MANE Select
- NM_001961
- dbSNP
- rs2230561
- Type
- single nucleotide variant
- Location
- chr19:3982969 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.97 · 26 PDB
- Residue 150
- the tr-type g domain
Similar variants
- EEF2 p.Arg150His Uncertain significance ★ ⚠ same residue
- EEF2 p.Ala237Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala238Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala338Gly Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala624Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala808Val Uncertain significance ★★ ⚠ same type
- EEF2 p.Arg633His Uncertain significance ★★ ⚠ same type
- EEF2 p.Arg647His 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/eef2-p-arg150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown