ATP9A p.Ala484=
c.1452C>T · rs57906305 · VCV784411
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.42%, afr) — 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 -5.8 | GERP -3.5 |
| Overall | ||
| CADD | 2.527 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.42%
African / African-American · 4,815/75,014 alleles
Filtering AF
6.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.21%
Overall
0.331%
5,350/1,614,124 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.42% | 16 |
| Remaining individualsnot grpmax-eligible | 0.41% | 244 |
| Admixed American | 0.337% | 297 |
| Middle Eastern | 0.231% | 433 |
| Finnishnot grpmax-eligible | 0.00937% | 10,672 |
| South Asian | 0.00769% | 13,011 |
| European (non-Finnish) | 0.00424% | 23,600 |
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
- ATP9A
- Protein
- p.Ala484=
- Coding
- c.1452C>T
- MANE Select
- NM_006045
- dbSNP
- rs57906305
- Type
- single nucleotide variant
- Location
- chr20:51656992 (GRCh38)
- Gene constraint
- LOEUF 0.455 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.28 · 4 PDB
- Residue 484
- a UniProt-annotated variant site (in nedgba; results in the formation of aggregated puncta distributed in the cytoplasm); a UniProt-annotated variant site (in nedgba; severely reduced mrna expression in homozygous patient cells); a UniProt-annotated variant site (in nedgba)
Similar variants
- ATP9A p.Ala607Pro Uncertain significance ★★ ⚠ same type
- ATP9A p.Asp197Asn Uncertain significance ★★ ⚠ same type
- ATP9A p.Met524Val Uncertain significance ★★ ⚠ same type
- ATP9A p.Gly32Val Benign ★★ ⚠ same type
- ATP9A p.Ile463= Likely benign ★★ same type
- ATP9A p.Ile992= Benign ★★ same type
- ATP9A p.Leu210= Benign ★★ same type
- ATP9A p.Ser386= Likely benign ★★ 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/atp9a-p-ala484 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown