EPM2A p.Val22=
c.66G>A · rs1057522731 · VCV387226
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,257,990)
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 0.41 | GERP -1.3, phastCons 0.99 |
| Overall | ||
| CADD | 8.739 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,257,990). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- EPM2A
- Protein
- p.Val22=
- Coding
- c.66G>A
- MANE Select
- NM_005670
- dbSNP
- rs1057522731
- Type
- single nucleotide variant
- Location
- chr6:145735433 (GRCh38)
- Gene constraint
- LOEUF 1.191 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 34.25 · 2 PDB
- Residue 22
- the 'disordered' region; the cbm20 domain; a β-strand
Similar variants
- EPM2A p.Val22Glu Uncertain significance ★ same residue
- EPM2A p.Val22Leu Uncertain significance ★ same residue
- EPM2A c.301+1G>T Pathogenic ★★ same type
- EPM2A c.302-1G>C Pathogenic/Likely pathogenic ★★ same type
- EPM2A c.302-2A>G Pathogenic ★★ same type
- EPM2A p.Arg108Cys Pathogenic/Likely pathogenic ★★ same type
- EPM2A p.Arg171His Pathogenic/Likely pathogenic ★★ same type
- EPM2A p.Arg241Ter Pathogenic/Likely 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/epm2a-p-val22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown