CSNK2B p.Pro172=
c.516C>T · VCV3341901
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
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 -7.5 | GERP -4.9 |
| Overall | ||
| CADD | 6.526 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,084 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000717%
Overall
0.00118%
19/1,612,848 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,542 |
| European (non-Finnish) | 0.00144% | 69,412 |
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.Pro172=
- Coding
- c.516C>T
- MANE Select
- NM_001320
- Type
- single nucleotide variant
- Location
- chr6:31669467 (GRCh38)
- Gene constraint
- LOEUF 0.237 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 93.70 · 10 PDB
- Residue 172
- a UniProt-annotated variant site (in pobinds; associated in cis with c-86); an α-helix
Similar variants
- CSNK2B p.Pro172Arg Uncertain significance ★ ⚠ same residue
- 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
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-pro172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown