CSNK1D
casein kinase 1 delta, the group of casein kinase 1 family
Basic information
Region (hg38): 17:82239023-82273700
Links
Phenotypes
GenCC
Source:
- advanced sleep phase syndrome (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Advanced sleep phase syndrome, familial, 2 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 15800623; 23636092 |
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 CSNK1D 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 | 7 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 7 | 1 |
Variants in CSNK1D
This is a list of pathogenic ClinVar variants found in the CSNK1D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-82239966-G-A | CSNK1D-related disorder | Likely benign (Aug 30, 2019) | ||
| 17-82240011-G-A | CSNK1D-related disorder | Likely benign (Mar 24, 2024) | ||
| 17-82240042-A-G | CSNK1D-related disorder | Likely benign (Jun 11, 2019) | ||
| 17-82244838-G-A | CSNK1D-related disorder | Likely benign (Dec 19, 2019) | ||
| 17-82248917-G-A | Likely benign (Apr 01, 2022) | |||
| 17-82248937-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 17-82249433-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 17-82249464-G-C | not specified | Uncertain significance (Dec 18, 2023) | ||
| 17-82249478-G-A | not specified | Uncertain significance (Apr 26, 2024) | ||
| 17-82249492-G-C | CSNK1D-related disorder | Likely benign (Feb 16, 2019) | ||
| 17-82249556-C-T | not specified | Uncertain significance (Jun 13, 2023) | ||
| 17-82249572-G-A | not specified | Uncertain significance (Mar 18, 2024) | ||
| 17-82249576-G-A | Benign (Jul 13, 2018) | |||
| 17-82249578-C-T | Likely benign (May 01, 2024) | |||
| 17-82251400-G-A | CSNK1D-related disorder | Likely benign (Sep 18, 2019) | ||
| 17-82251436-C-T | CSNK1D-related disorder | Likely benign (Aug 06, 2019) | ||
| 17-82255531-G-A | Likely benign (Jun 01, 2022) | |||
| 17-82255552-G-A | Benign/Likely benign (Aug 01, 2024) | |||
| 17-82265736-T-C | Advanced sleep phase syndrome 2 | Pathogenic (May 01, 2013) | ||
| 17-82265743-T-C | Advanced sleep phase syndrome 2 | Pathogenic (May 01, 2013) | ||
| 17-82265784-G-A | not specified | Uncertain significance (Mar 21, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CSNK1D | protein_coding | protein_coding | ENST00000314028 | 9 | 34709 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00423 | 125738 | 0 | 3 | 125741 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.70 | 136 | 258 | 0.527 | 0.0000181 | 2659 |
| Missense in Polyphen | 42 | 109.9 | 0.38216 | 1183 | ||
| Synonymous | -2.09 | 137 | 109 | 1.25 | 0.00000773 | 836 |
| Loss of Function | 4.00 | 1 | 20.6 | 0.0486 | 0.00000115 | 226 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000552 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000552 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential serine/threonine-protein kinase that regulates diverse cellular growth and survival processes including Wnt signaling, DNA repair and circadian rhythms. It can phosphorylate a large number of proteins. Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. Phosphorylates connexin-43/GJA1, MAP1A, SNAPIN, MAPT/TAU, TOP2A, DCK, HIF1A, EIF6, p53/TP53, DVL2, DVL3, ESR1, AIB1/NCOA3, DNMT1, PKD2, YAP1, PER1 and PER2. Central component of the circadian clock. In balance with PP1, determines the circadian period length through the regulation of the speed and rhythmicity of PER1 and PER2 phosphorylation. Controls PER1 and PER2 nuclear transport and degradation. YAP1 phosphorylation promotes its SCF(beta-TRCP) E3 ubiquitin ligase-mediated ubiquitination and subsequent degradation. DNMT1 phosphorylation reduces its DNA-binding activity. Phosphorylation of ESR1 and AIB1/NCOA3 stimulates their activity and coactivation. Phosphorylation of DVL2 and DVL3 regulates WNT3A signaling pathway that controls neurite outgrowth. EIF6 phosphorylation promotes its nuclear export. Triggers down-regulation of dopamine receptors in the forebrain. Activates DCK in vitro by phosphorylation. TOP2A phosphorylation favors DNA cleavable complex formation. May regulate the formation of the mitotic spindle apparatus in extravillous trophoblast. Modulates connexin-43/GJA1 gap junction assembly by phosphorylation. Probably involved in lymphocyte physiology. Regulates fast synaptic transmission mediated by glutamate. {ECO:0000269|PubMed:10606744, ECO:0000269|PubMed:12270943, ECO:0000269|PubMed:14761950, ECO:0000269|PubMed:16027726, ECO:0000269|PubMed:17562708, ECO:0000269|PubMed:17962809, ECO:0000269|PubMed:19043076, ECO:0000269|PubMed:19339517, ECO:0000269|PubMed:20041275, ECO:0000269|PubMed:20048001, ECO:0000269|PubMed:20407760, ECO:0000269|PubMed:20637175, ECO:0000269|PubMed:20696890, ECO:0000269|PubMed:20699359, ECO:0000269|PubMed:21084295, ECO:0000269|PubMed:21422228, ECO:0000269|PubMed:23636092}.;
- Disease
- DISEASE: Advanced sleep phase syndrome, familial, 2 (FASPS2) [MIM:615224]: A disorder characterized by very early sleep onset and offset. Individuals are 'morning larks' with a 4 hours advance of the sleep, temperature and melatonin rhythms. {ECO:0000269|PubMed:15800623, ECO:0000269|PubMed:23636092}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Circadian rhythm - Homo sapiens (human);Gap junction - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Hedgehog signaling pathway - Homo sapiens (human);WNT-Core;Integrated Breast Cancer Pathway;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Melatonin metabolism and effects;Wnt Signaling Pathway;Hedgehog Signaling Pathway;Circadian Clock;Vesicle-mediated transport;regulation of ck1/cdk5 by type 1 glutamate receptors;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;IL-7 signaling;Regulation of PLK1 Activity at G2/M Transition;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;JAK STAT pathway and regulation;EPO signaling;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;VEGF;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Degradation of beta catenin;FoxO family signaling;Hedgehog signaling events mediated by Gli proteins;p53 pathway;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.546
Intolerance Scores
- loftool
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.31
Haploinsufficiency Scores
- pHI
- 0.951
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.586
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Csnk1d
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype;
Gene ontology
- Biological process
- G2/M transition of mitotic cell cycle;positive regulation of protein phosphorylation;protein phosphorylation;microtubule nucleation;Golgi organization;regulation of G2/M transition of mitotic cell cycle;Wnt signaling pathway;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;circadian regulation of gene expression;protein localization to Golgi apparatus;regulation of circadian rhythm;COPII vesicle coating;spindle assembly;protein localization to cilium;protein localization to centrosome;positive regulation of canonical Wnt signaling pathway;ciliary basal body-plasma membrane docking;positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation;non-motile cilium assembly;cellular response to nerve growth factor stimulus;positive regulation of non-canonical Wnt signaling pathway
- Cellular component
- Golgi membrane;nucleus;nucleoplasm;cytoplasm;Golgi apparatus;centrosome;spindle;cytosol;spindle microtubule;plasma membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;neuron projection;perinuclear region of cytoplasm
- Molecular function
- protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;peptide binding;cadherin binding;tau-protein kinase activity