GeneBe

CSNK1D

protein-coding

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

Gene summary

This gene is a member of the casein kinase I (CKI) gene family whose members have been implicated in the control of cytoplasmic and nuclear processes, including DNA replication and repair. The encoded protein may also be involved in the regulation of apoptosis, circadian rhythm, microtubule dynamics, chromosome segregation, and p53-mediated effects on growth. The encoded protein is highly similar to the mouse and rat CK1 delta homologs. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]

MANE transcript

NM_001893.6

Inheritance

AD

ClinVar variants

P:2U:39B:14

Top phenotype

Advanced sleep phase syndrome, familial, 2

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr17:82,239,023-82,273,700

External References & Databases

Ensembl (ENSG00000141551)NCBI Gene (1453)OMIM (600864)HGNC:2452GenCCUniProt (P48730)AlphaFoldClinVar (CSNK1D)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~34.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

advanced sleep phase syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015609

Submitter: Orphanet

Clinical Genomic Database (CGD)

Advanced sleep phase syndrome, familial, 2AD

Manifestation: Neurologic

Intervention: General

Rationale: 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

Refs: 15800623; 23636092Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CSNK1D variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 35
CSNK1D-related disorderTotal: 8
not providedTotal: 8
Advanced sleep phase syndrome 2Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001893.6. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
11
clinvar
2
clinvar
 15
missense
2
clinvar
34
clinvar
1
clinvar
 37
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total203912255

Highest pathogenic variant AF is 0.000001858743

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001893.6RefSeqNP_001884.29MANE Select
ENST00000314028.11EnsemblENSP00000324464.69MANE Select
NM_001363749.2RefSeqNP_001350678.19Standard
NM_139062.4RefSeqNP_620693.19Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Circadian rhythm - Homo sapiens (human)
  • Gap junction - Homo sapiens (human)
  • Hippo signaling pathway - Homo sapiens (human)
  • Hedgehog signaling pathway - Homo sapiens (human)
  • WNT-Core

Biological Process

  • G2/M transition of mitotic cell cycle
  • positive regulation of protein phosphorylation
  • protein phosphorylation
  • microtubule nucleation
  • Golgi organization

Molecular Function

  • protein kinase activity
  • protein serine/threonine kinase activity
  • protein binding
  • ATP binding
  • peptide binding

Cellular Component

  • Golgi membrane
  • nucleus
  • nucleoplasm
  • cytoplasm
  • Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000314028
Coding exons
9
Length
34709
Individuals with no LoFs
125738
Homozygous LoFs
0
Heterozygous LoFs
3
Defined
125741
p
0.0000119
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.701362580.5270.00001812659
Missense (PolyPhen)42109.90.382161183
Synonymous-2.091371091.250.00000773836
Loss of Function4.00120.60.04860.00000115226

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish0.0000990.000099rare
East Asian0.0000550.000054rare
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec
0.546

Intolerance Scores

RVIS EVS
-0.56
RVIS percentile EVS
19.31

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.999

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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