ATP2B2 p.Asp820=
c.2460C>T · rs182259252 · VCV2040592
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.397%, eas)
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 -9.5 | GERP -3.9 |
| Overall | ||
| CADD | 1.372 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.397%
East Asian · 178/44,880 alleles
Filtering AF
0.349%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.331%
Overall
0.0136%
220/1,612,278 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.397% | 252 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,289 |
| Admixed American | 0.00666% | 15,006 |
| South Asian | 0.00659% | 15,180 |
| African / African-American | 0.00266% | 37,530 |
| Finnishnot grpmax-eligible | 0.00161% | 62,198 |
| European (non-Finnish) | 0.000847% | 117,998 |
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
- ATP2B2
- Protein
- p.Asp820=
- Coding
- c.2460C>T
- MANE Select
- NM_001001331
- dbSNP
- rs182259252
- Type
- single nucleotide variant
- Location
- chr3:10346082 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.83
- Residue 820
- a binding site; a UniProt-annotated variant site (in dfna82)
Similar variants
- ATP2B2 c.2136+1G>A Pathogenic/Likely pathogenic ★★ same type
- ATP2B2 p.Arg1132Ter Pathogenic/Likely pathogenic ★★ same type
- ATP2B2 p.Glu457Lys Likely pathogenic ★★ same type
- ATP2B2 p.Gly821Arg Pathogenic ★★ same type
- ATP2B2 p.Thr503Met Pathogenic/Likely pathogenic ★★ same type
- ATP2B2 c.2316+5G>A Uncertain significance ★★ same type
- ATP2B2 c.3420+1998G>T Uncertain significance ★★ same type
- ATP2B2 p.Ala135Val Uncertain significance ★★ ⚠ 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/atp2b2-p-asp820 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown