ATP2B4 p.Pro558=
c.1674C>T · rs147713701 · VCV2639819
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.173%, 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 -20 | GERP -3.8 |
| Overall | ||
| CADD | 0.628 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.173%
African / African-American · 130/75,048 alleles
Filtering AF
0.149%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.14%
Overall
0.00935%
151/1,614,160 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.173% | 577 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.0133% | 7,502 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| South Asian | 0.0022% | 45,537 |
| European (non-Finnish) | 0.000339% | 295,009 |
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
- ATP2B4
- Protein
- p.Pro558=
- Coding
- c.1674C>T
- MANE Select
- NM_001684
- dbSNP
- rs147713701
- Type
- single nucleotide variant
- Location
- chr1:203709417 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.71 · 2 PDB
Similar variants
- ATP2B4 p.Arg554Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg624Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg732Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg993Gly Uncertain significance ★★ same type
- ATP2B4 p.Asn851Ser Uncertain significance ★★ same type
- ATP2B4 p.Asp333Gly Uncertain significance ★★ same type
- ATP2B4 p.Asp502Asn Uncertain significance ★★ same type
- ATP2B4 p.Gly634Arg 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/atp2b4-p-pro558 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown