CSNK1G2
protein-codingcasein kinase 1 gamma 2, the group of casein kinase 1 family
Gene summary
Enables protein serine/threonine kinase activity. Predicted to be involved in endocytosis; positive regulation of canonical Wnt signaling pathway; and signal transduction. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~40.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CSNK1G2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001319.7. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 39 | 2 | 41 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 41 | 4 | 0 | 45 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001310.3 | 11 | MANE Select | |
| Ensembl | ENSP00000255641.7 | 11 | MANE Select | |
| Ensembl | ENSP00000480052.1 | 3 | Standard | |
| Ensembl | ENSP00000480185.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Hedgehog signaling pathway - Homo sapiens (human)
- Hedgehog Signaling Pathway
- Signaling by WNT
- Signal Transduction
- Metabolism of lipids
Biological Process
- protein phosphorylation
- endocytosis
- signal transduction
- Wnt signaling pathway
- peptidyl-serine phosphorylation
Molecular Function
- magnesium ion binding
- protein serine/threonine kinase activity
- protein binding
- ATP binding
- peptide binding
Cellular Component
- nucleus
- cytoplasm
- cytosol
- plasma membrane
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000255641
- Coding exons
- 11
- Length
- 40150
- Individuals with no LoFs
- 123266
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 123269
- p
- 0.0000122
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.80 | 134 | 261 | 0.513 | 0.0000193 | 2681 |
| Missense (PolyPhen) | 50 | 142.19 | 0.35165 | 1345 | ||
| Synonymous | -1.93 | 142 | 116 | 1.23 | 0.00000925 | 768 |
| Loss of Function | 3.79 | 1 | 18.6 | 0.0536 | 7.90e-7 | 243 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000063 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Serine/threonine-protein kinase. Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. It can phosphorylate a large number of proteins. Participates in Wnt signaling. Phosphorylates COL4A3BP/CERT, MTA1 and SMAD3. Involved in brain development and vesicular trafficking and neurotransmitter releasing from small synaptic vesicles. Regulates fast synaptic transmission mediated by glutamate. SMAD3 phosphorylation promotes its ligand-dependent ubiquitination and subsequent proteasome degradation, thus inhibiting SMAD3-mediated TGF-beta responses. Hyperphosphorylation of the serine-repeat motif of COL4A3BP/CERT leads to its inactivation by dissociation from the Golgi complex, thus down-regulating ER-to-Golgi transport of ceramide and sphingomyelin synthesis. Triggers PER1 proteasomal degradation probably through phosphorylation. {ECO:0000269|PubMed:15077195, ECO:0000269|PubMed:15342122, ECO:0000269|PubMed:15917222, ECO:0000269|PubMed:18794808, ECO:0000269|PubMed:19005213}.;
Recessive Scores
- pRec
- 0.169
Intolerance Scores
- LoFtool
- 0.297
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 37.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.978
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |