ATP2A3 p.Ser385=
c.1155G>C · rs1032107053 · VCV3050071
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0687%, eas)
Conditions
1
ATP2A3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.90 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.4 |
| Overall | ||
| CADD | 2.864 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0687%
East Asian · 28/40,760 alleles
Filtering AF
0.0488%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0421%
Overall
0.00426%
66/1,547,650 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0687% | 1,456 |
| Remaining individualsnot grpmax-eligible | 0.0585% | 1,711 |
| Admixed American | 0.00393% | 25,454 |
| South Asian | 0.00119% | 83,998 |
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
- ATP2A3
- Protein
- p.Ser385=
- Coding
- c.1155G>C
- MANE Select
- NM_005173
- dbSNP
- rs1032107053
- Type
- single nucleotide variant
- Location
- chr17:3945089 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.75
- Residue 385
- the 'interaction with phospholamban 1' region
Disease context
ATP2A3-related disorder
Similar variants
- ATP2A3 c.1095+9C>T Likely benign same condition
- ATP2A3 c.1419+10G>A Benign same condition
- ATP2A3 c.1420-4G>A Likely benign same condition
- ATP2A3 c.2863-5G>A Benign same condition
- ATP2A3 c.*14A>G Benign same condition
- ATP2A3 c.*19A>G Benign same condition
- ATP2A3 p.Ala223= Likely benign same condition
- ATP2A3 p.Ala331= Likely benign same condition
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/atp2a3-p-ser385 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown