ATP2B2 p.Ser989=
c.2967G>A · rs61736452 · VCV785032
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.46%, afr) — too common for a highly-penetrant pathogenic allele
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 -16 | GERP -3.9 |
| Overall | ||
| CADD | 1.534 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.46%
African / African-American · 4,093/75,006 alleles
Filtering AF
5.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.26%
Overall
0.291%
4,705/1,614,136 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.46% | 18 |
| Remaining individualsnot grpmax-eligible | 0.397% | 252 |
| Admixed American | 0.365% | 274 |
| Middle Eastern | 0.247% | 404 |
| European (non-Finnish) | 0.0102% | 9,834 |
| South Asian | 0.00769% | 13,011 |
| Finnishnot grpmax-eligible | 0.00469% | 21,343 |
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.Ser989=
- Coding
- c.2967G>A
- MANE Select
- NM_001001331
- dbSNP
- rs61736452
- Type
- single nucleotide variant
- Location
- chr3:10340655 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.83
- Residue 989
- 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-ser989 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown