EEF2 c.400+3A>G
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.16 | GERP -1.1, phastCons 0.42 |
| Non-coding constraint | Z 0.56 | 1 kb window · o/e 0.97 · regional · uncalibrated |
| Overall | ||
| CADD | 12.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,968 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.00143%
23/1,613,324 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,989 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,824 |
| European (non-Finnish) | 0.00136% | 73,724 |
| African / African-American | 0.00134% | 74,876 |
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
- Coding
- c.400+3A>G
- MANE Select
- NM_001961
- Type
- single nucleotide variant
- Location
- chr19:3983107 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.97 · 26 PDB
Similar variants
- 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
- EEF2 p.Arg726Trp 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-c-400-plus-3a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown