EIF2S2 p.Val44=
c.132G>C · rs201521464 · VCV732335
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.07%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -2.4 |
| Overall | ||
| CADD | 7.234 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.07%
Admixed American · 42/60,012 alleles
Filtering AF
0.0532%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0473%
Overall
0.00328%
53/1,614,082 alleles · ultra-rare
exomes 18/1,461,776 · genomes 35/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.07% | 1,429 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,682 |
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
- EIF2S2
- Protein
- p.Val44=
- Coding
- c.132G>C
- MANE Select
- NM_003908
- dbSNP
- rs201521464
- Type
- single nucleotide variant
- Location
- chr20:34105429 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.98 · 17 PDB
- Residue 44
- the 'disordered' region
Similar variants
- EIF2S2 p.Ala56Gly Uncertain significance ★ ⚠ same type
- EIF2S2 p.Arg182Gln Uncertain significance ★ ⚠ same type
- EIF2S2 p.Arg329Cys Uncertain significance ★ ⚠ same type
- EIF2S2 p.Asn161His Uncertain significance ★ ⚠ same type
- EIF2S2 p.Asn185Ser Uncertain significance ★ ⚠ same type
- EIF2S2 p.Asp53Gly Uncertain significance ★ ⚠ same type
- EIF2S2 p.Glu112Asp Uncertain significance ★ ⚠ same type
- EIF2S2 p.Glu138Asp 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/eif2s2-p-val44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown