EIF2B1 p.Val259=
c.777C>T · rs1955102772 · VCV1616596
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 -3.1 | GERP -3.6 |
| Overall | ||
| CADD | 0.191 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,034 alleles
Overall
6.84e-05%
1/1,461,754 alleles · very rare
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
- EIF2B1
- Protein
- p.Val259=
- Coding
- c.777C>T
- MANE Select
- NM_001414
- dbSNP
- rs1955102772
- Type
- single nucleotide variant
- Location
- chr12:123621897 (GRCh38)
- Gene constraint
- LOEUF 1.06 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.67 · 38 PDB
Similar variants
- EIF2B1 p.Arg147Ter Pathogenic/Likely pathogenic ★★ same type
- EIF2B1 p.Tyr275Cys Pathogenic/Likely pathogenic ★★ same type
- EIF2B1 c.627+3A>G Uncertain significance ★★ same type
- EIF2B1 c.-183C>G Uncertain significance ★★ same type
- EIF2B1 c.*506C>T Uncertain significance ★★ same type
- EIF2B1 p.Ala129Thr Uncertain significance ★★ same type
- EIF2B1 p.Ala144Thr Uncertain significance ★★ ⚠ same type
- EIF2B1 p.Ala260Thr Uncertain significance ★★ ⚠ 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/eif2b1-p-val259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown