EIF3A p.Lys388=
c.1164A>G · rs144766795 · VCV737391
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.755%, 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 1.1 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 9.533 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.755%
African / African-American · 559/74,010 alleles
Filtering AF
0.703%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.683%
Overall
0.0407%
650/1,595,350 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.755% | 132 |
| Admixed American | 0.0736% | 1,358 |
| Remaining individualsnot grpmax-eligible | 0.0665% | 1,504 |
| Middle Eastern | 0.05% | 2,002 |
| South Asian | 0.00112% | 89,400 |
| European (non-Finnish) | 0.000257% | 389,229 |
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
- EIF3A
- Protein
- p.Lys388=
- Coding
- c.1164A>G
- MANE Select
- NM_003750
- dbSNP
- rs144766795
- Type
- single nucleotide variant
- Location
- chr10:119061287 (GRCh38)
- Gene constraint
- LOEUF 0.18 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.62 · 30 PDB
- Residue 388
- the pci domain; an α-helix
Similar variants
- EIF3A p.Ala1358= Benign ★★ same type
- EIF3A p.Arg1046Trp Likely benign ★★ ⚠ same type
- EIF3A p.Arg406= Benign/Likely benign ★★ same type
- EIF3A p.Arg803Lys Benign ★★ ⚠ same type
- EIF3A p.Asp993Glu Benign ★★ ⚠ same type
- EIF3A p.Arg1273Ser Likely pathogenic ★ ⚠ same type
- EIF3A p.Ala1354Ser Uncertain significance ★ ⚠ same type
- EIF3A p.Ala181Gly 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/eif3a-p-lys388 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown