ATP2A2 p.Cys498=
c.1494T>C · rs1879138571 · VCV3039727
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
ATP2A2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.18 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -3.5 |
| Overall | ||
| CADD | 7.407 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,030 alleles
Overall
0.000657%
1/152,178 alleles · very rare
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
- ATP2A2
- Protein
- p.Cys498=
- Coding
- c.1494T>C
- MANE Select
- NM_170665
- dbSNP
- rs1879138571
- Type
- single nucleotide variant
- Location
- chr12:110339355 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.46 · 15 PDB
- Residue 498
- a β-strand
Disease context
ATP2A2-related disorder
Similar variants
- ATP2A2 p.Ala803Thr Pathogenic/Likely pathogenic ★★ same condition
- ATP2A2 p.Asn767Ser Pathogenic/Likely pathogenic ★★ same condition
- ATP2A2 p.Ile348Thr Pathogenic/Likely pathogenic ★★ same condition
- ATP2A2 p.Met1Leu Pathogenic ★★ same condition
- ATP2A2 c.118+2T>C Likely pathogenic ★ same condition
- ATP2A2 p.Arg559Ter Pathogenic ★ same condition
- ATP2A2 p.Arg677Ter Pathogenic ★ same condition
- ATP2A2 p.Cys268Phe Likely pathogenic ★ same condition
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/atp2a2-p-cys498 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown