ATP2B4 p.Val342Ala
c.1025T>C · rs145963279 · VCV703837
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.89%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.185 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.9 | GERP -3.8 |
| Regional constraint | o/e 0.77 | unconstrained · MANE · 6,862 bp · p 0.00083 · regional, not allelic |
| Overall | ||
| CADD | 0.672 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.89%
African / African-American · 1,415/75,040 alleles
Filtering AF
1.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.77%
Overall
0.101%
1,637/1,614,128 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.89% | 53 |
| Admixed American | 0.153% | 652 |
| Remaining individualsnot grpmax-eligible | 0.128% | 781 |
| Middle Eastern | 0.0826% | 1,211 |
| European (non-Finnish) | 0.00364% | 27,442 |
| South Asian | 0.0022% | 45,539 |
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.Val342Ala
- Coding
- c.1025T>C
- MANE Select
- NM_001684
- dbSNP
- rs145963279
- Type
- single nucleotide variant
- Location
- chr1:203703739 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.71 · 2 PDB
Similar variants
- 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
- 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-val342ala (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown