CSNK2B p.Ser2=
c.6C>T · rs1801756577 · VCV3048258
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
1
CSNK2B-related disorder
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 1.1 | GERP -0.52, phastCons 1 |
| Overall | ||
| CADD | 14.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,352 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,460,918 alleles · very rare
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
- CSNK2B
- Protein
- p.Ser2=
- Coding
- c.6C>T
- MANE Select
- NM_001320
- dbSNP
- rs1801756577
- Type
- single nucleotide variant
- Location
- chr6:31666837 (GRCh38)
- Gene constraint
- LOEUF 0.237 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 93.70 · 10 PDB
- Residue 2
- a modified residue (n-acetylserine); a modified residue (phosphoserine; by autocatalysis)
Disease context
CSNK2B-related disorder
Similar variants
- CSNK2B c.175+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CSNK2B c.291+1G>T Likely pathogenic ★★ same condition
- CSNK2B p.Arg111Pro Pathogenic ★★ same condition
- CSNK2B p.Arg47Ter Pathogenic ★★ same condition
- CSNK2B p.Gln102Ter Pathogenic ★★ same condition
- CSNK2B p.Glu5Ter Pathogenic/Likely pathogenic ★★ same condition
- CSNK2B p.His165Arg Pathogenic/Likely pathogenic ★★ same condition
- CSNK2B p.Met97Ile Likely pathogenic ★★ same condition
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/csnk2b-p-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown