ATP2A2 p.Pro193=
c.579C>T · rs371699814 · VCV2167432
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0108%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.094 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.7 | GERP -5.1 |
| Overall | ||
| CADD | 6.993 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0108%
European (non-Finnish) · 127/1,179,984 alleles
Filtering AF
0.00919%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00863%
Overall
0.00923%
149/1,614,038 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0108% | 9,291 |
| Admixed American | 0.01% | 9,999 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| South Asian | 0.00769% | 13,004 |
| African / African-American | 0.004% | 25,010 |
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
- ATP2A2
- Protein
- p.Pro193=
- Coding
- c.579C>T
- MANE Select
- NM_170665
- dbSNP
- rs371699814
- Type
- single nucleotide variant
- Location
- chr12:110326424 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.46 · 15 PDB
- Residue 193
- an α-helix
Similar variants
- ATP2A2 p.Ala803Thr Pathogenic/Likely pathogenic ★★ same type
- ATP2A2 p.Asn767Ser Pathogenic/Likely pathogenic ★★ same type
- ATP2A2 p.Asp702Asn Pathogenic ★★ same type
- ATP2A2 p.Gly211Asp Pathogenic ★★ same type
- ATP2A2 p.Ile348Thr Pathogenic/Likely pathogenic ★★ same type
- ATP2A2 p.Met1Leu Pathogenic ★★ same type
- ATP2A2 p.Met1Val Pathogenic ★★ same type
- ATP2A2 p.Pro602Leu Pathogenic ★★ 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/atp2a2-p-pro193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown