ATP2B2 p.Ala642=
c.1926G>A · rs1159414805 · VCV1370080
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, 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 -11 | GERP -5.1 |
| Overall | ||
| CADD | 0.357 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,864 alleles
Filtering AF
0.00884%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.00267%
39/1,461,606 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,608 |
| South Asian | 0.00549% | 18,210 |
| European (non-Finnish) | 0.00203% | 49,167 |
| Admixed American | 0.00167% | 60,028 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,498 |
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.Ala642=
- Coding
- c.1926G>A
- MANE Select
- NM_001001331
- dbSNP
- rs1159414805
- Type
- single nucleotide variant
- Location
- chr3:10358901 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.83
Similar variants
- ATP2B2 p.Ala642Glu Uncertain significance ★ ⚠ same residue
- ATP2B2 p.Ala642fs Pathogenic ★ same residue
- 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
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-ala642 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown