CSNK1G2
casein kinase 1 gamma 2, the group of casein kinase 1 family
Basic information
Region (hg38): 19:1941172-1981338
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 2 | 0 |
Variants in CSNK1G2
This is a list of pathogenic ClinVar variants found in the CSNK1G2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-1969842-G-A | not specified | Uncertain significance (Apr 13, 2022) | ||
| 19-1969857-G-A | not specified | Likely benign (Apr 10, 2023) | ||
| 19-1969870-C-T | not specified | Uncertain significance (Apr 08, 2022) | ||
| 19-1978706-C-G | not specified | Uncertain significance (May 13, 2024) | ||
| 19-1978934-C-T | not specified | Uncertain significance (Jul 11, 2023) | ||
| 19-1979015-A-C | not specified | Uncertain significance (Sep 07, 2022) | ||
| 19-1979174-C-T | not specified | Uncertain significance (Aug 02, 2021) | ||
| 19-1979189-G-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 19-1979219-C-T | not specified | Uncertain significance (Feb 02, 2024) | ||
| 19-1979226-G-A | not specified | Uncertain significance (Nov 05, 2021) | ||
| 19-1979327-G-A | Likely benign (Sep 01, 2023) | |||
| 19-1979364-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
| 19-1979371-C-T | not specified | Uncertain significance (May 24, 2024) | ||
| 19-1979590-G-C | not specified | Uncertain significance (Jan 02, 2024) | ||
| 19-1979800-C-T | not specified | Uncertain significance (May 08, 2024) | ||
| 19-1979929-G-T | not specified | Uncertain significance (Jul 19, 2022) | ||
| 19-1979942-C-T | not specified | Uncertain significance (Jun 22, 2021) | ||
| 19-1980193-G-A | not specified | Uncertain significance (May 06, 2024) |
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