ATP2A3 p.Ser915=
c.2745C>T · VCV3971350
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0197%, mid)
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 -3.3 | GERP -3.8 |
| Overall | ||
| CADD | 1.852 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0197%
Middle Eastern · 1/5,072 alleles
Filtering AF
0.00256%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00163%
Overall
0.00201%
32/1,589,716 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0197% | 5,072 |
| African / African-American | 0.00672% | 14,872 |
| Admixed American | 0.00527% | 18,991 |
| European (non-Finnish) | 0.00188% | 53,154 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,400 |
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.Ser915=
- Coding
- c.2745C>T
- MANE Select
- NM_005173
- Type
- single nucleotide variant
- Location
- chr17:3929445 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.75
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.Arg560= Benign/Likely 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
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-ser915 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown