ATP2C2 p.Arg640=
c.1920C>T · rs759660872 · VCV3033252
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Conditions
1
ATP2C2-related disorder
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 -3.8 | GERP -2.5 |
| Overall | ||
| CADD | 0.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000806%
13/1,613,876 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| African / African-American | 0.00801% | 12,483 |
| Admixed American | 0.00167% | 60,002 |
| European (non-Finnish) | 0.000424% | 235,985 |
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
- ATP2C2
- Protein
- p.Arg640=
- Coding
- c.1920C>T
- MANE Select
- NM_014861
- dbSNP
- rs759660872
- Type
- single nucleotide variant
- Location
- chr16:84453226 (GRCh38)
- Gene constraint
- LOEUF 1.712 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.13
Disease context
ATP2C2-related disorder
Similar variants
- ATP2C2 c.2580+1G>A Uncertain significance same condition
- ATP2C2 p.Ala223Asp Uncertain significance ⚠ same condition
- ATP2C2 c.1210-10C>T Likely benign same condition
- ATP2C2 c.1504-3A>G Likely benign same condition
- ATP2C2 c.1980+6C>T Likely benign same condition
- ATP2C2 c.2217-5C>T Likely benign same condition
- ATP2C2 c.2333+112T>A Likely benign same condition
- ATP2C2 c.2333+148A>G Likely benign same condition
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/atp2c2-p-arg640 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown