ATP8B2 p.Arg952=
c.2856G>A · VCV3974397
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.73 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -1.9 |
| Overall | ||
| CADD | 7.202 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00724%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00676%
Overall
0.00694%
112/1,614,030 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| European (non-Finnish) | 0.00864% | 11,569 |
| African / African-American | 0.00534% | 18,726 |
| South Asian | 0.00329% | 30,361 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
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
- ATP8B2
- Protein
- p.Arg952=
- Coding
- c.2856G>A
- MANE Select
- NM_001370597
- Type
- single nucleotide variant
- Location
- chr1:154346308 (GRCh38)
- Gene constraint
- LOEUF 0.624 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.24
Similar variants
- ATP8B2 p.Asn380= Benign ★★ same type
- ATP8B2 p.Asn579= Benign ★★ same type
- ATP8B2 c.-37-294G>T Uncertain significance ★ same type
- ATP8B2 p.Ala1153Ser Uncertain significance ★ same type
- ATP8B2 p.Ala456Thr Uncertain significance ★ same type
- ATP8B2 p.Ala589Val Uncertain significance ★ same type
- ATP8B2 p.Ala716Val Uncertain significance ★ same type
- ATP8B2 p.Ala754Gly 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/atp8b2-p-arg952 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown