EFTUD2 p.Lys142=
c.426G>A · rs1555569606 · VCV435031
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 22.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EFTUD2
- Protein
- p.Lys142=
- Coding
- c.426G>A
- MANE Select
- NM_004247
- dbSNP
- rs1555569606
- Type
- single nucleotide variant
- Location
- chr17:44883649 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 89.94 · 72 PDB
- Residue 142
- the tr-type g domain; a β-strand; a binding site
Similar variants
- EFTUD2 p.Lys142Arg Uncertain significance ★ ⚠ same residue
- EFTUD2 p.Lys142fs Pathogenic ★ 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-lys142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown