ATP2A3 p.Arg560=
c.1680C>T · rs150386916 · VCV768822
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.536%, nfe)
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 0.25 | GERP -1.8, phastCons 0.92 |
| Overall | ||
| CADD | 6.653 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.536%
European (non-Finnish) · 6,322/1,179,938 alleles
Filtering AF
0.525%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.52%
Overall
0.431%
6,948/1,613,856 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.536% | 187 |
| Finnishnot grpmax-eligible | 0.354% | 282 |
| Remaining individualsnot grpmax-eligible | 0.338% | 296 |
| Amishnot grpmax-eligible | 0.219% | 456 |
| South Asian | 0.105% | 949 |
| African / African-American | 0.0786% | 1,272 |
| Admixed American | 0.05% | 2,001 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
| East Asian | 0.00223% | 44,888 |
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.Arg560=
- Coding
- c.1680C>T
- MANE Select
- NM_005173
- dbSNP
- rs150386916
- Type
- single nucleotide variant
- Location
- chr17:3941520 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.75
- Residue 560
- a binding site
Similar variants
- ATP2A3 c.2525-6C>G Likely benign ★★ same type
- ATP2A3 p.Ala299= Likely benign ★★ same type
- ATP2A3 p.Arg491= Benign ★★ same type
- ATP2A3 p.Arg674Cys Likely benign ★★ ⚠ same type
- ATP2A3 p.Ile716= Benign/Likely benign ★★ same type
- ATP2A3 p.Ser877= Benign ★★ same type
- ATP2A3 c.2611-1G>C Uncertain significance ★ same type
- ATP2A3 p.Ala112Thr 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/atp2a3-p-arg560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown