ATP8A2 p.Ser1046=
c.3138G>A · rs149257236 · VCV1599885
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.196%, 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 -4.1 | GERP -4.7 |
| Overall | ||
| CADD | 4.049 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.196%
African / African-American · 147/75,012 alleles
Filtering AF
0.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.16%
Overall
0.0111%
179/1,613,990 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.196% | 510 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,464 |
| Admixed American | 0.0217% | 4,616 |
| South Asian | 0.0011% | 91,040 |
| European (non-Finnish) | 0.000339% | 294,991 |
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.Ser1046=
- Coding
- c.3138G>A
- MANE Select
- NM_016529
- dbSNP
- rs149257236
- Type
- single nucleotide variant
- Location
- chr13:25862363 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 81.12
- Residue 1046
- a UniProt-annotated variant site (in camrq4; uncertain significance)
Similar variants
- 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
- ATP8A2 p.Ala335Thr 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-ser1046 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown