ATP2C2 p.Ala667=
c.2001G>A · rs142596443 · VCV712738
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.22%, amr)
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 -13 | GERP -4.9 |
| Overall | ||
| CADD | 0.085 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.22%
Admixed American · 1,316/59,154 alleles
Filtering AF
2.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.08%
Overall
0.233%
3,755/1,610,788 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 2.22% | 45 |
| East Asian | 2.17% | 46 |
| Remaining individualsnot grpmax-eligible | 0.302% | 332 |
| South Asian | 0.185% | 540 |
| European (non-Finnish) | 0.0895% | 1,117 |
| Middle Eastern | 0.084% | 1,190 |
| African / African-American | 0.0588% | 1,701 |
| Finnishnot grpmax-eligible | 0.0125% | 7,999 |
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.Ala667=
- Coding
- c.2001G>A
- MANE Select
- NM_014861
- dbSNP
- rs142596443
- Type
- single nucleotide variant
- Location
- chr16:84454838 (GRCh38)
- Gene constraint
- LOEUF 1.712 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.13
Similar variants
- ATP2C2 p.Ala813Val Uncertain significance ★★ ⚠ same type
- ATP2C2 p.Tyr877Ser Uncertain significance ★★ ⚠ same type
- ATP2C2 c.2148-9C>G Benign ★★ same type
- ATP2C2 c.2334-8C>T Benign ★★ same type
- ATP2C2 c.2481+7G>T Benign ★★ same type
- ATP2C2 c.2482-19C>G Benign ★★ same type
- ATP2C2 c.2482-2A>C Benign ★★ same type
- ATP2C2 p.Ala138Thr Benign ★★ 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/atp2c2-p-ala667 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown