EFTUD2 p.Ala328=
c.984C>T · rs117507317 · VCV789453
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.18%, eas)
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 -3.1 | GERP -5.6 |
| Overall | ||
| CADD | 5.503 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.18%
East Asian · 527/44,778 alleles
Filtering AF
1.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.06%
Overall
0.0396%
638/1,612,740 alleles · low-frequency
exomes 563/1,460,430 · genomes 75/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.18% | 85 |
| South Asian | 0.0406% | 2,460 |
| Remaining individualsnot grpmax-eligible | 0.0385% | 2,600 |
| Middle Eastern | 0.0165% | 6,054 |
| European (non-Finnish) | 0.0039% | 25,634 |
| Admixed American | 0.00334% | 29,979 |
| Finnishnot grpmax-eligible | 0.00157% | 63,878 |
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
- EFTUD2
- Protein
- p.Ala328=
- Coding
- c.984C>T
- MANE Select
- NM_004247
- dbSNP
- rs117507317
- Type
- single nucleotide variant
- Location
- chr17:44872456 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 89.94 · 72 PDB
- Residue 328
- the tr-type g domain; an α-helix
Similar variants
- EFTUD2 p.Ala328Ser Uncertain significance ★ ⚠ same residue
- EFTUD2 p.Ala328Thr Uncertain significance ★ ⚠ same residue
- EFTUD2 c.1058+1G>A Pathogenic ★★ same type
- EFTUD2 c.1414-2A>G Pathogenic/Likely pathogenic ★★ same type
- EFTUD2 c.1607+1G>T Likely pathogenic ★★ same type
- EFTUD2 c.1962+1G>A Pathogenic/Likely pathogenic ★★ same type
- EFTUD2 c.2133-2A>G Pathogenic/Likely pathogenic ★★ same type
- EFTUD2 c.2562-2A>G Pathogenic/Likely pathogenic ★★ 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/eftud2-p-ala328 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown