EIF3D p.Pro233=
c.699T>C · rs138620321 · VCV739587
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.365%, 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 -3.8 | GERP -3.7 |
| Overall | ||
| CADD | 2.665 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.365%
African / African-American · 274/75,032 alleles
Filtering AF
0.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.316%
Overall
0.0187%
302/1,614,152 alleles · rare
exomes 136/1,461,890 · genomes 166/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.365% | 274 |
| Admixed American | 0.0233% | 4,287 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| European (non-Finnish) | 0.000169% | 590,016 |
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
- EIF3D
- Protein
- p.Pro233=
- Coding
- c.699T>C
- MANE Select
- NM_003753
- dbSNP
- rs138620321
- Type
- single nucleotide variant
- Location
- chr22:36519417 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.36 · 28 PDB
- Residue 233
- an α-helix
Similar variants
- EIF3D c.711+7G>A Benign ★★ same type
- EIF3D c.712-10C>T Benign ★★ same type
- EIF3D c.1077-1G>C Uncertain significance ★ same type
- EIF3D p.Ala92Val Uncertain significance ★ ⚠ same type
- EIF3D p.Arg165Gly Uncertain significance ★ ⚠ same type
- EIF3D p.Arg222His Uncertain significance ★ ⚠ same type
- EIF3D p.Arg26Gln Uncertain significance ★ ⚠ same type
- EIF3D p.Arg410His 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/eif3d-p-pro233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown