EFTUD2 p.Pro470=
c.1410T>G · rs73986406 · VCV2727279
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, afr)
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 -2.6 | GERP -5.5 |
| Overall | ||
| CADD | 8.293 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
African / African-American · 18/75,008 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00118%
19/1,612,974 alleles · ultra-rare
exomes 10/1,460,646 · genomes 9/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.024% | 4,167 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,442 |
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.Pro470=
- Coding
- c.1410T>G
- MANE Select
- NM_004247
- dbSNP
- rs73986406
- Type
- single nucleotide variant
- Location
- chr17:44863658 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 89.94 · 72 PDB
- Residue 470
- a β-strand
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-pro470 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown