CSNK2A1 p.Ser2=
c.6G>A · rs773390884 · VCV390679
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00187%, nfe)
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 5.9 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 16.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00187%
European (non-Finnish) · 22/1,179,412 alleles
Filtering AF
0.00122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00149%
24/1,612,824 alleles · very rare
exomes 20/1,460,660 · genomes 4/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00187% | 53,610 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,420 |
| South Asian | 0.0011% | 90,942 |
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
- CSNK2A1
- Protein
- p.Ser2=
- Coding
- c.6G>A
- MANE Select
- NM_177559
- dbSNP
- rs773390884
- Type
- single nucleotide variant
- Location
- chr20:508546 (GRCh38)
- Gene constraint
- LOEUF 0.274 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 90.78 · 316 PDB
Similar variants
- CSNK2A1 p.Arg107Ter Likely pathogenic ★★ same type
- CSNK2A1 p.Arg134Ter Pathogenic/Likely pathogenic ★★ same type
- CSNK2A1 p.Arg191Gln Pathogenic ★★ same type
- CSNK2A1 p.Arg280Ter Pathogenic ★★ same type
- CSNK2A1 p.Arg306Ter Pathogenic/Likely pathogenic ★★ same type
- CSNK2A1 p.Arg312Gln Pathogenic/Likely pathogenic ★★ same type
- CSNK2A1 p.Arg312Trp Pathogenic/Likely pathogenic ★★ same type
- CSNK2A1 p.Arg333Ter 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/csnk2a1-p-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown