ATP2A2 p.Asp702=
c.2106T>C · rs373988845 · VCV744819
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.112%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.343 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -5.1 |
| Overall | ||
| CADD | 0.174 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.112%
African / African-American · 84/75,068 alleles
Filtering AF
0.0926%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0854%
Overall
0.00582%
94/1,614,238 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.112% | 894 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| Admixed American | 0.00333% | 30,015 |
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.Asp702=
- Coding
- c.2106T>C
- MANE Select
- NM_170665
- dbSNP
- rs373988845
- Type
- single nucleotide variant
- Location
- chr12:110342236 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.46 · 15 PDB
- Residue 702
- a binding site; a UniProt-annotated variant site (in dd); a UniProt-annotated variant site (in dd; moderate form)
Similar variants
- ATP2A2 p.Asp702Asn Pathogenic ★★ same residue
- ATP2A2 p.Ala803Thr Pathogenic/Likely pathogenic ★★ same type
- ATP2A2 p.Asn767Ser Pathogenic/Likely 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-asp702 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown