ATP2A2 p.Ala87=
c.261C>A · rs1592795871 · VCV730135
Likely benign
Single submitter
Classification
Likely benign
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 | 0.072 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.4 | 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
- ATP2A2
- Protein
- p.Ala87=
- Coding
- c.261C>A
- MANE Select
- NM_170665
- dbSNP
- rs1592795871
- Type
- single nucleotide variant
- Location
- chr12:110292061 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.46 · 15 PDB
- Residue 87
- an α-helix; a UniProt-annotated variant site (in dd)
Similar variants
- ATP2A2 p.Ala803Thr Pathogenic/Likely pathogenic ★★ same type
- ATP2A2 p.Asn767Ser Pathogenic/Likely pathogenic ★★ same type
- ATP2A2 p.Asp702Asn Pathogenic ★★ same type
- ATP2A2 p.Gly211Asp Pathogenic ★★ same type
- ATP2A2 p.Ile348Thr Pathogenic/Likely pathogenic ★★ same type
- ATP2A2 p.Met1Leu Pathogenic ★★ same type
- ATP2A2 p.Met1Val Pathogenic ★★ same type
- ATP2A2 p.Pro602Leu 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/atp2a2-p-ala87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown