ATP2B2 p.His520=
c.1560C>T · rs547169657 · VCV1654459
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0659%, 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 5.1 | GERP 0.76, phastCons 1 |
| Overall | ||
| CADD | 8.137 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0659%
South Asian · 60/91,078 alleles
Filtering AF
0.0525%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0476%
Overall
0.00384%
62/1,614,184 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0659% | 1,518 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,254 |
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
- ATP2B2
- Protein
- p.His520=
- Coding
- c.1560C>T
- MANE Select
- NM_001001331
- dbSNP
- rs547169657
- Type
- single nucleotide variant
- Location
- chr3:10371908 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.83
Similar variants
- ATP2B2 c.2136+1G>A Pathogenic/Likely pathogenic ★★ same type
- ATP2B2 p.Arg1132Ter Pathogenic/Likely pathogenic ★★ same type
- ATP2B2 p.Glu457Lys Likely pathogenic ★★ same type
- ATP2B2 p.Gly821Arg Pathogenic ★★ same type
- ATP2B2 p.Thr503Met Pathogenic/Likely pathogenic ★★ same type
- ATP2B2 c.2316+5G>A Uncertain significance ★★ same type
- ATP2B2 c.3420+1998G>T Uncertain significance ★★ same type
- ATP2B2 p.Ala135Val 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/atp2b2-p-his520 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown