CSNK2A2 p.Ser195=
c.585A>G · rs2292027 · VCV1278914
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.67%, 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 -1.7 | GERP -5.1 |
| Overall | ||
| CADD | 6.776 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.67%
East Asian · 2,097/44,876 alleles
Filtering AF
4.51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.44%
Overall
0.159%
2,559/1,614,070 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.67% | 21 |
| South Asian | 0.225% | 444 |
| Remaining individualsnot grpmax-eligible | 0.165% | 607 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0676% | 1,480 |
| Middle Eastern | 0.0495% | 2,020 |
| Admixed American | 0.0183% | 5,456 |
| European (non-Finnish) | 0.00992% | 10,085 |
| African / African-American | 0.00267% | 37,523 |
| Finnishnot grpmax-eligible | 0.00156% | 64,042 |
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
- CSNK2A2
- Protein
- p.Ser195=
- Coding
- c.585A>G
- MANE Select
- NM_001896
- dbSNP
- rs2292027
- Type
- single nucleotide variant
- Location
- chr16:58167724 (GRCh38)
- Gene constraint
- LOEUF 0.424 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 94.91 · 59 PDB
- Residue 195
- the protein kinase domain
Similar variants
- CSNK2A2 c.104+271G>A Benign ★★ same type
- CSNK2A2 c.104+50C>T Benign ★★ same type
- CSNK2A2 c.369+188A>G Benign ★★ same type
- CSNK2A2 c.370-122A>G Benign ★★ same type
- CSNK2A2 c.514-60T>C Benign ★★ same type
- CSNK2A2 c.727-29T>G Benign ★★ same type
- CSNK2A2 c.828-140C>A Benign ★★ same type
- CSNK2A2 c.828-58G>A 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/csnk2a2-p-ser195 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown