EFTUD2 p.Val113=
c.339G>A · rs371529062 · VCV1950519
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.27 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -3.6 |
| Overall | ||
| CADD | 9.945 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,876 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000372%
6/1,613,484 alleles · very rare
exomes 4/1,461,348 · genomes 2/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,719 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
| South Asian | 0.0011% | 91,050 |
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.Val113=
- Coding
- c.339G>A
- MANE Select
- NM_004247
- dbSNP
- rs371529062
- Type
- single nucleotide variant
- Location
- chr17:44885267 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 89.94 · 72 PDB
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-val113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown