CSNK1D

casein kinase 1 delta, the group of casein kinase 1 family

Basic information

Region (hg38): 17:82239022-82273700

Links

ENSG00000141551 ∙ NCBI:1453 ∙ OMIM:600864 ∙ HGNC:2452 ∙ Uniprot:P48730 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• advanced sleep phase syndrome (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the CSNK1D gene.

• not provided (4 variants)
• Inborn genetic diseases (1 variants)

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				3	1	4
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	3	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)
17-82240042-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)
17-82249464-G-C		not specified	Uncertain significance (Dec 18, 2023)
17-82249492-G-C		CSNK1D-related disorder	Likely benign (Feb 16, 2019)
17-82249556-C-T		not specified	Uncertain significance (Jun 13, 2023)
17-82249576-G-A			Benign (Jul 13, 2018)
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 (Feb 01, 2023)
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)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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