EIF4A2 p.Arg366Ter
c.1096C>T · rs1213509261 · VCV2572859
Uncertain significance
Single submitter
Classification
Uncertain significance
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 in a LoF-intolerant gene |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (11 of 11) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 39.0 | 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
- EIF4A2
- Protein
- p.Arg366Ter
- Coding
- c.1096C>T
- MANE Select
- NM_001967
- dbSNP
- rs1213509261
- Type
- single nucleotide variant
- Location
- chr3:186789141 (GRCh38)
- Gene constraint
- LOEUF 0.298 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 1 PDB
- Residue 366
- the helicase c-terminal domain
Similar variants
- EIF4A2 p.Gly362Ser Pathogenic ★★ same type
- EIF4A2 p.Ile278Thr Uncertain significance ★★ ⚠ same type
- EIF4A2 c.517+1G>T Likely pathogenic ★ same type
- EIF4A2 p.Asp338Tyr Likely pathogenic ★ same type
- EIF4A2 p.Gly161Arg Likely pathogenic ★ same type
- EIF4A2 p.Gly161Trp Likely pathogenic ★ same type
- EIF4A2 p.Thr216Ala Pathogenic ★ same type
- EIF4A2 p.Thr216Ile 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/eif4a2-p-arg366ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown