CSNK2B p.Ter216Ser
c.647G>C · VCV3360835
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
stop-loss
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | stop-loss | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.7 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 18.32 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CSNK2B
- Protein
- p.Ter216Ser
- Coding
- c.647G>C
- MANE Select
- NM_001320
- Type
- single nucleotide variant
- Location
- chr6:31669925 (GRCh38)
- Gene constraint
- LOEUF 0.237 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 93.70 · 10 PDB
Similar variants
- CSNK2B c.175+1G>A Pathogenic/Likely pathogenic ★★ same type
- CSNK2B c.291+1G>A Pathogenic/Likely pathogenic ★★ same type
- CSNK2B c.291+1G>T Likely pathogenic ★★ same type
- CSNK2B c.292-2A>C Pathogenic/Likely pathogenic ★★ same type
- CSNK2B c.292-2A>G Pathogenic/Likely pathogenic ★★ same type
- CSNK2B c.292-2A>T Pathogenic/Likely pathogenic ★★ same type
- CSNK2B c.367+1G>C Pathogenic ★★ same type
- CSNK2B c.557+1G>C 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/csnk2b-p-ter216ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown