EIF2B5 p.Ser157Ter
c.470C>G · rs2473661266 · VCV2736131
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
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. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 16 |
| 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 | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- EIF2B5
- Protein
- p.Ser157Ter
- Coding
- c.470C>G
- MANE Select
- NM_003907
- dbSNP
- rs2473661266
- Type
- single nucleotide variant
- Location
- chr3:184137769 (GRCh38)
- Gene constraint
- LOEUF 0.544 · pLI 0.16 (gnomAD)
- Structure
- AlphaFold pLDDT 79.35 · 37 PDB
- Residue 157
- a β-strand
Similar variants
- EIF2B5 p.Ala403Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- EIF2B5 p.Arg113Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- EIF2B5 p.Arg113His Pathogenic ★★ ⚠ same type
- EIF2B5 p.Arg121Ter Pathogenic/Likely pathogenic ★★ same type
- EIF2B5 p.Arg136Cys Pathogenic/Likely pathogenic ★★ same type
- EIF2B5 p.Arg136His Pathogenic ★★ same type
- EIF2B5 p.Arg195Cys Likely pathogenic ★★ ⚠ same type
- EIF2B5 p.Arg195His 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/eif2b5-p-ser157ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown