ATP2C2 p.Val191=
c.573C>A · rs375031013 · VCV2723351
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.01%, 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 -4.6 | GERP -5.1 |
| Overall | ||
| CADD | 0.311 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,008 alleles
Filtering AF
0.00538%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00498%
Overall
0.00558%
90/1,614,030 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,001 |
| European (non-Finnish) | 0.00661% | 15,128 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| African / African-American | 0.00267% | 37,461 |
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.Val191=
- Coding
- c.573C>A
- MANE Select
- NM_014861
- dbSNP
- rs375031013
- Type
- single nucleotide variant
- Location
- chr16:84415540 (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-val191 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown