CSNK1G2
Basic information
Region (hg38): 19:1941172-1981338
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (35 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK1G2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001319.7. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 33 | 35 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 33 | 4 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CSNK1G2 | protein_coding | protein_coding | ENST00000255641 | 11 | 40150 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.991 | 0.00862 | 123266 | 0 | 3 | 123269 | 0.0000122 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.80 | 134 | 261 | 0.513 | 0.0000193 | 2681 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000633 | 0.0000620 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000183 | 0.0000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- Hedgehog signaling pathway - Homo sapiens (human);Hedgehog Signaling Pathway;Signaling by WNT;Signal Transduction;Metabolism of lipids;Metabolism;Disassembly of the destruction complex and recruitment of AXIN to the membrane;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;Sphingolipid de novo biosynthesis;Sphingolipid metabolism;VEGF;TCF dependent signaling in response to WNT;FoxO family signaling;Hedgehog signaling events mediated by Gli proteins;p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.169
Intolerance Scores
- loftool
- 0.297
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 37.32
Haploinsufficiency Scores
- pHI
- 0.515
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.530
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.978
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Csnk1g2
- Phenotype
Gene ontology
- Biological process
- protein phosphorylation;endocytosis;signal transduction;Wnt signaling pathway;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;sphingolipid biosynthetic process;protein autophosphorylation;positive regulation of canonical Wnt signaling pathway
- Cellular component
- nucleus;cytoplasm;cytosol;plasma membrane;membrane
- Molecular function
- magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding;peptide binding;phosphoprotein binding