ATP8A2 p.Ala302=
c.906G>A · rs9581388 · VCV1164903
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 12.9%, sas) — 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 -0.3 | GERP -3.8, phastCons 0.005 |
| Overall | ||
| CADD | 7.577 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
12.9%
South Asian · 11,771/90,962 alleles
Filtering AF
12.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 12.7%
Overall
4.52%
72,909/1,613,252 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 12.9% | 8 |
| African / African-American | 11.5% | 9 |
| Middle Eastern | 9.85% | 10 |
| Amishnot grpmax-eligible | 9.12% | 11 |
| Admixed American | 8.24% | 12 |
| Ashkenazi Jewishnot grpmax-eligible | 5.96% | 17 |
| Remaining individualsnot grpmax-eligible | 5.28% | 19 |
| Finnishnot grpmax-eligible | 4.91% | 20 |
| European (non-Finnish) | 3.28% | 31 |
| East Asian | 0.0892% | 1,122 |
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
- ATP8A2
- Protein
- p.Ala302=
- Coding
- c.906G>A
- MANE Select
- NM_016529
- dbSNP
- rs9581388
- Type
- single nucleotide variant
- Location
- chr13:25551352 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 81.12
Similar variants
- ATP8A2 p.Ala302Glu Uncertain significance ★ ⚠ same residue
- ATP8A2 c.1782+2T>C Pathogenic ★★ same type
- ATP8A2 c.2212-1G>C Pathogenic ★★ same type
- ATP8A2 c.3272+1G>A Pathogenic/Likely pathogenic ★★ same type
- ATP8A2 c.77-2A>G Pathogenic/Likely pathogenic ★★ same type
- ATP8A2 p.Arg586Ter Pathogenic/Likely pathogenic ★★ same type
- ATP8A2 p.Asp765Tyr Likely pathogenic ★★ same type
- ATP8A2 p.Ala1091Val 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/atp8a2-p-ala302 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown