ATP2C1 p.Ser595=
c.1785A>G · rs200047787 · VCV737151
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.073 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.096 | GERP -4.3, phastCons 0.013 |
| Overall | ||
| CADD | 8.322 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,072 alleles
Filtering AF
0.0152%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0144%
Overall
0.0136%
219/1,613,246 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,036 |
| European (non-Finnish) | 0.0171% | 5,839 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,804 |
| Finnishnot grpmax-eligible | 0.00625% | 16,005 |
| South Asian | 0.00329% | 30,359 |
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
- ATP2C1
- Protein
- p.Ser595=
- Coding
- c.1785A>G
- MANE Select
- NM_001378687
- dbSNP
- rs200047787
- Type
- single nucleotide variant
- Location
- chr3:130980625 (GRCh38)
- Gene constraint
- LOEUF 0.402 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.33 · 11 PDB
- Residue 595
- a β-strand
Similar variants
- ATP2C1 c.1308+1G>T Pathogenic ★★ same type
- ATP2C1 c.2058-1G>A Pathogenic ★★ same type
- ATP2C1 p.Arg153Ter Pathogenic ★★ same type
- ATP2C1 p.Arg799Ter Pathogenic ★★ same type
- ATP2C1 p.Arg806Ter Pathogenic ★★ same type
- ATP2C1 p.Asn738Ser Likely pathogenic ★★ same type
- ATP2C1 p.Ile580Val Likely pathogenic ★★ ⚠ same type
- ATP2C1 p.Tyr452Ter Pathogenic/Likely pathogenic ★★ 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/atp2c1-p-ser595 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown