ATP4A p.Ile503=
c.1509C>A · rs2230181 · VCV1598599
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 42.7%, mid) — too common for a highly-penetrant pathogenic allele
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 1.6 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 11.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
42.7%
Middle Eastern · 1,964/4,598 alleles
Filtering AF
41.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 40.5%
Overall
37.5%
569,888/1,518,700 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 42.7% | 2 |
| Finnishnot grpmax-eligible | 41.6% | 2 |
| Amishnot grpmax-eligible | 40.5% | 2 |
| European (non-Finnish) | 39.7% | 3 |
| South Asian | 39.5% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 37.8% | 3 |
| Remaining individualsnot grpmax-eligible | 37% | 3 |
| East Asian | 21.7% | 5 |
| Admixed American | 20.7% | 5 |
| African / African-American | 18.8% | 5 |
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
- ATP4A
- Protein
- p.Ile503=
- Coding
- c.1509C>A
- MANE Select
- NM_000704
- dbSNP
- rs2230181
- Type
- single nucleotide variant
- Location
- chr19:35557839 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.70
Similar variants
- ATP4A p.Ala104Thr Uncertain significance ★★ ⚠ same type
- ATP4A p.Ala104Val Uncertain significance ★★ ⚠ same type
- ATP4A p.Ala119Thr Uncertain significance ★★ ⚠ same type
- ATP4A p.Ala170Ser Uncertain significance ★★ ⚠ same type
- ATP4A p.Ala90Thr Uncertain significance ★★ ⚠ same type
- ATP4A p.Arg607Trp Uncertain significance ★★ ⚠ same type
- ATP4A p.Arg660His Uncertain significance ★★ ⚠ same type
- ATP4A p.Arg668Cys 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/atp4a-p-ile503 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown