ATP2B4 p.Val500=
c.1500C>T · rs1480374823 · VCV2727165
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 0.27 | GERP 0.91, phastCons 0.29 |
| Overall | ||
| CADD | 6.889 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,890 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.00062%
10/1,614,030 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,890 |
| Admixed American | 0.00167% | 59,992 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| European (non-Finnish) | 0.000593% | 168,577 |
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
- ATP2B4
- Protein
- p.Val500=
- Coding
- c.1500C>T
- MANE Select
- NM_001684
- dbSNP
- rs1480374823
- Type
- single nucleotide variant
- Location
- chr1:203708047 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.71 · 2 PDB
Similar variants
- ATP2B4 p.Val500Ala Uncertain significance ★ same residue
- ATP2B4 p.Arg554Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg624Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg732Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg993Gly Uncertain significance ★★ same type
- ATP2B4 p.Asn851Ser Uncertain significance ★★ same type
- ATP2B4 p.Asp333Gly Uncertain significance ★★ same type
- ATP2B4 p.Asp502Asn 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/atp2b4-p-val500 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown