EFTUD2 p.Ile449=
c.1347T>A · rs200923569 · VCV2990844
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 -2.3 | GERP -5.5 |
| Overall | ||
| CADD | 1.771 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,004 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000558%
9/1,614,082 alleles · very rare
exomes 6/1,461,864 · genomes 3/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,001 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| European (non-Finnish) | 0.000169% | 590,012 |
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.Ile449=
- Coding
- c.1347T>A
- MANE Select
- NM_004247
- dbSNP
- rs200923569
- Type
- single nucleotide variant
- Location
- chr17:44863721 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 89.94 · 72 PDB
- Residue 449
- an α-helix
Similar variants
- EFTUD2 p.Ile449Phe 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
- EFTUD2 c.702+1G>T 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-ile449 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown