EIF2D p.Pro350=
c.1050G>A · rs41274816 · VCV2639862
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.346%, mid)
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 -8.2 | GERP -4.1 |
| Overall | ||
| CADD | 2.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.346%
Middle Eastern · 21/6,062 alleles
Filtering AF
0.308%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.305%
Overall
0.276%
4,456/1,614,134 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.346% | 289 |
| Remaining individualsnot grpmax-eligible | 0.334% | 299 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| European (non-Finnish) | 0.317% | 316 |
| Admixed American | 0.228% | 438 |
| Finnishnot grpmax-eligible | 0.175% | 572 |
| South Asian | 0.17% | 588 |
| Ashkenazi Jewishnot grpmax-eligible | 0.111% | 897 |
| African / African-American | 0.0666% | 1,500 |
| East Asian | 0.00223% | 44,874 |
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
- EIF2D
- Protein
- p.Pro350=
- Coding
- c.1050G>A
- MANE Select
- NM_006893
- dbSNP
- rs41274816
- Type
- single nucleotide variant
- Location
- chr1:206599735 (GRCh38)
- Gene constraint
- LOEUF 0.862 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.23 · 3 PDB
Similar variants
- EIF2D p.Pro350Leu Uncertain significance ★ ⚠ same residue
- EIF2D p.Ala149Ser Uncertain significance ★ ⚠ same type
- EIF2D p.Ala150Val Uncertain significance ★ ⚠ same type
- EIF2D p.Ala24Thr Uncertain significance ★ ⚠ same type
- EIF2D p.Ala499Val Uncertain significance ★ ⚠ same type
- EIF2D p.Arg20Ser Uncertain significance ★ ⚠ same type
- EIF2D p.Arg508Gln Uncertain significance ★ ⚠ same type
- EIF2D p.Arg527Gln 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/eif2d-p-pro350 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown