CSNK1D p.Phe288=
c.864C>T · rs148622760 · VCV3040908
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.12%, amr)
Conditions
1
CSNK1D-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 -1.6 | GERP -3.7 |
| Overall | ||
| CADD | 11.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.12%
Admixed American · 72/59,986 alleles
Filtering AF
0.0977%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0895%
Overall
0.0611%
986/1,613,982 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.12% | 833 |
| Remaining individualsnot grpmax-eligible | 0.0864% | 1,157 |
| South Asian | 0.0856% | 1,168 |
| European (non-Finnish) | 0.0655% | 1,527 |
| Middle Eastern | 0.0164% | 6,084 |
| African / African-American | 0.00801% | 12,483 |
| East Asian | 0.00445% | 22,447 |
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
- CSNK1D
- Protein
- p.Phe288=
- Coding
- c.864C>T
- MANE Select
- NM_001893
- dbSNP
- rs148622760
- Type
- single nucleotide variant
- Location
- chr17:82251400 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 82.10 · 53 PDB
- Residue 288
- the 'centrosomal localization signal (cls)' region
Disease context
CSNK1D-related disorder
Similar variants
- CSNK1D c.1198-7C>T Likely benign same condition
- CSNK1D p.Arg417Cys Likely benign same condition
- CSNK1D p.Gly332= Likely benign same condition
- CSNK1D p.Leu276= Likely benign same condition
- CSNK1D p.Ser406= Likely benign same condition
- CSNK1D p.Ala304= Benign ★★ same type
- CSNK1D p.Cys71= Benign/Likely benign ★★ same type
- CSNK1D p.Ala30Val Uncertain significance ★ ⚠ 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/csnk1d-p-phe288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown