EIF2B3 p.Arg57=
c.169A>C · rs1644475566 · VCV2751547
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 7.7 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 13.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Overall
0.000186%
3/1,613,370 alleles · ultra-rare
exomes 2/1,461,452 · genomes 1/151,918 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| Finnishnot grpmax-eligible | 0.00157% | 63,598 |
| European (non-Finnish) | 8.47e-05% | 1,179,979 |
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
- EIF2B3
- Protein
- p.Arg57=
- Coding
- c.169A>C
- MANE Select
- NM_020365
- dbSNP
- rs1644475566
- Type
- single nucleotide variant
- Location
- chr1:44978440 (GRCh38)
- Gene constraint
- LOEUF 0.522 · pLI 0.93 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.51 · 37 PDB
Similar variants
- EIF2B3 p.Ala87Val Pathogenic/Likely pathogenic ★★ same type
- EIF2B3 p.Arg225Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- EIF2B3 p.Arg225Trp Likely pathogenic ★★ same type
- EIF2B3 p.Ile346Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- EIF2B3 p.Val30Ala Pathogenic/Likely pathogenic ★★ same type
- EIF2B3 c.784+4A>C Uncertain significance ★★ same type
- EIF2B3 c.*55C>T Uncertain significance ★★ same type
- EIF2B3 p.Ala280Thr 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/eif2b3-p-arg57 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown