EIF2B1 p.Val183=
c.549C>T · rs139071270 · VCV2977464
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, 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 -1.4 | GERP -3.6 |
| Overall | ||
| CADD | 1.409 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,920 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00198%
32/1,613,986 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,763 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,828 |
| South Asian | 0.00329% | 30,362 |
| European (non-Finnish) | 0.0011% | 90,768 |
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.Val183=
- Coding
- c.549C>T
- MANE Select
- NM_001414
- dbSNP
- rs139071270
- Type
- single nucleotide variant
- Location
- chr12:123626427 (GRCh38)
- Gene constraint
- LOEUF 1.06 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.67 · 38 PDB
- Residue 183
- an α-helix; a UniProt-annotated variant site (in vwm1)
Similar variants
- EIF2B1 p.Val183Phe Pathogenic same residue
- 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
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-val183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown