ATP2C2 p.Ser742=
c.2226C>T · rs144698981 · VCV721014
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.666%, eas)
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 -20 | GERP -4.9 |
| Overall | ||
| CADD | 0.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.666%
East Asian · 299/44,888 alleles
Filtering AF
0.604%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.58%
Overall
0.101%
1,623/1,614,212 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.666% | 150 |
| Middle Eastern | 0.627% | 160 |
| African / African-American | 0.372% | 269 |
| Remaining individualsnot grpmax-eligible | 0.118% | 845 |
| South Asian | 0.0801% | 1,248 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0777% | 1,287 |
| European (non-Finnish) | 0.0678% | 1,475 |
| Admixed American | 0.055% | 1,819 |
| Finnishnot grpmax-eligible | 0.00625% | 16,009 |
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.Ser742=
- Coding
- c.2226C>T
- MANE Select
- NM_014861
- dbSNP
- rs144698981
- Type
- single nucleotide variant
- Location
- chr16:84459279 (GRCh38)
- Gene constraint
- LOEUF 1.712 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.13
Similar variants
- ATP2C2 p.Ser742Cys Uncertain significance ★ ⚠ same residue
- 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
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-ser742 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown