ATP2A3 p.Pro42=
c.126G>T · rs73971770 · VCV722163
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.446%, afr)
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 -5.6 | GERP -3.6 |
| Overall | ||
| CADD | 3.861 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.446%
African / African-American · 330/74,004 alleles
Filtering AF
0.406%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.391%
Overall
0.0233%
366/1,569,694 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.446% | 224 |
| Remaining individualsnot grpmax-eligible | 0.0312% | 3,200 |
| Admixed American | 0.03% | 3,331 |
| European (non-Finnish) | 8.64e-05% | 1,157,338 |
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.Pro42=
- Coding
- c.126G>T
- MANE Select
- NM_005173
- dbSNP
- rs73971770
- Type
- single nucleotide variant
- Location
- chr17:3953703 (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-pro42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown