ATP2B4 p.Ser1204Pro
c.3610T>C · rs765803167 · VCV3131577
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0447%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.233 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 1.11 | unconstrained · MANE · 207 bp · p 0.3 · regional, not allelic |
| Overall | ||
| CADD | 21.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0447%
East Asian · 20/44,722 alleles
Filtering AF
0.0296%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0247%
Overall
0.00143%
23/1,604,256 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0447% | 2,236 |
| European (non-Finnish) | 0.000255% | 391,426 |
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.Ser1204Pro
- Coding
- c.3610T>C
- MANE Select
- NM_001684
- dbSNP
- rs765803167
- Type
- single nucleotide variant
- Location
- chr1:203739846 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.71 · 2 PDB
Similar variants
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- 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
- ATP2B4 p.Gly634Arg 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-ser1204pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown