EIF2B2 p.Asp314=
c.942C>T · rs772125418 · VCV2825388
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor loss, 43 bp away · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.30 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 9.848 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,086 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000136%
Overall
0.000342%
5/1,461,870 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,543 |
| European (non-Finnish) | 0.000254% | 393,335 |
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
- EIF2B2
- Protein
- p.Asp314=
- Coding
- c.942C>T
- MANE Select
- NM_014239
- dbSNP
- rs772125418
- Type
- single nucleotide variant
- Location
- chr14:75009074 (GRCh38)
- Gene constraint
- LOEUF 1.25 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.82 · 38 PDB
- Residue 314
- a β-strand
Similar variants
- EIF2B2 p.Asp314Ter Pathogenic ★ same residue
- EIF2B2 c.285-1G>A Likely pathogenic ★★ same type
- EIF2B2 c.832-2A>G Likely pathogenic ★★ same type
- EIF2B2 p.Arg172Ter Pathogenic/Likely pathogenic ★★ same type
- EIF2B2 p.Arg183Ter Pathogenic/Likely pathogenic ★★ same type
- EIF2B2 p.Glu213Gly Pathogenic ★★ same type
- EIF2B2 p.Glu304Ter Pathogenic/Likely pathogenic ★★ same type
- EIF2B2 p.Gly200Val 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/eif2b2-p-asp314 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown