ATP8A2 p.Thr154=
c.462A>C · rs201689401 · VCV1168393
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.318%, sas)
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 -1.1 | GERP -3.7 |
| Overall | ||
| CADD | 0.628 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.318%
South Asian · 285/89,638 alleles
Filtering AF
0.288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.276%
Overall
0.0318%
512/1,610,180 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.318% | 315 |
| Middle Eastern | 0.116% | 862 |
| Remaining individualsnot grpmax-eligible | 0.0433% | 2,310 |
| European (non-Finnish) | 0.0156% | 6,405 |
| Admixed American | 0.0101% | 9,908 |
| African / African-American | 0.00267% | 37,471 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
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.Thr154=
- Coding
- c.462A>C
- MANE Select
- NM_016529
- dbSNP
- rs201689401
- Type
- single nucleotide variant
- Location
- chr13:25532313 (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 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-thr154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown