EFTUD2 p.Leu461=
c.1383C>T · VCV3708360
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, 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 -3.3 | GERP -5.5 |
| Overall | ||
| CADD | 1.344 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/59,990 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.00105%
17/1,614,008 alleles · very rare
exomes 16/1,461,800 · genomes 1/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 29,995 |
| East Asian | 0.00223% | 44,898 |
| South Asian | 0.0022% | 45,540 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| African / African-American | 0.00133% | 74,928 |
| European (non-Finnish) | 0.000847% | 118,000 |
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.Leu461=
- Coding
- c.1383C>T
- MANE Select
- NM_004247
- Type
- single nucleotide variant
- Location
- chr17:44863685 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 89.94 · 72 PDB
- Residue 461
- an α-helix
Similar variants
- 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
- EFTUD2 c.703-2A>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-leu461 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown