EPM2A p.Ser330Arg
c.990C>A · VCV4541232
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.216 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -3.9 |
| Regional constraint | o/e 1.04 | unconstrained · MANE · 108 kb · p 0.41 · regional, not allelic |
| Overall | ||
| CADD | 0.012 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EPM2A
- Protein
- p.Ser330Arg
- Coding
- c.990C>A
- MANE Select
- NM_005670
- Type
- single nucleotide variant
- Location
- chr6:145627422 (GRCh38)
- Gene constraint
- LOEUF 1.191 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 34.25 · 2 PDB
- Residue 330
- the 'disordered' region
Similar variants
- EPM2A p.Ser330Ile 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
- EPM2A p.Gln293Leu 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-ser330arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown