CSNK1D (casein kinase 1 delta)

Gene

• Entrez ID: 1453
• Gene name: Casein kinase 1 delta
• Gene symbol: CSNK1D
• Synonyms: ASPS, CKI-delta, CKId, CKIdelta, FASPS2, HCKID
• Chromosome: 17
• Chromosome location: 17q25.3
• 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]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894561	T>C	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs397514693	T>C	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT001640	hsa-let-7b-5p	pSILAC, Proteomics;Other	18668040
MIRT016176	hsa-miR-590-3p	Sequencing	20371350
MIRT610084	hsa-miR-362-3p	HITS-CLIP	23824327
MIRT610085	hsa-miR-329-3p	HITS-CLIP	23824327
MIRT610086	hsa-miR-8485	HITS-CLIP	23824327
MIRT613748	hsa-miR-602	HITS-CLIP	23824327
MIRT736747	hsa-miR-1271-5p	PAR-CLIP	26701625
MIRT736859	hsa-miR-1273h-5p	PAR-CLIP	26701625
MIRT738179	hsa-miR-183-5p	PAR-CLIP	26701625
MIRT738981	hsa-miR-212-5p	PAR-CLIP	26701625
MIRT739749	hsa-miR-30b-3p	PAR-CLIP	26701625
MIRT739813	hsa-miR-30c-1-3p	PAR-CLIP	26701625
MIRT739856	hsa-miR-30c-2-3p	PAR-CLIP	26701625
MIRT740946	hsa-miR-3189-3p	PAR-CLIP	26701625
MIRT741759	hsa-miR-3622a-3p	PAR-CLIP	26701625
MIRT741767	hsa-miR-3622b-3p	PAR-CLIP	26701625
MIRT742251	hsa-miR-3689a-3p	PAR-CLIP	26701625
MIRT742321	hsa-miR-3689b-3p	PAR-CLIP	26701625
MIRT742391	hsa-miR-3689c	PAR-CLIP	26701625
MIRT743525	hsa-miR-4268	PAR-CLIP	26701625
MIRT744677	hsa-miR-4448	PAR-CLIP	26701625
MIRT749939	hsa-miR-5192	PAR-CLIP	26701625
MIRT751593	hsa-miR-593-5p	PAR-CLIP	26701625
MIRT753998	hsa-miR-6731-5p	PAR-CLIP	26701625
MIRT755063	hsa-miR-6765-3p	PAR-CLIP	26701625
MIRT755317	hsa-miR-6772-3p	PAR-CLIP	26701625
MIRT755490	hsa-miR-6779-5p	PAR-CLIP	26701625
MIRT755566	hsa-miR-6780a-5p	PAR-CLIP	26701625
MIRT755965	hsa-miR-6788-5p	PAR-CLIP	26701625
MIRT758200	hsa-miR-6878-5p	PAR-CLIP	26701625
MIRT760201	hsa-miR-8085	PAR-CLIP	26701625
MIRT760405	hsa-miR-887-5p	PAR-CLIP	26701625
MIRT760924	hsa-miR-96-5p	PAR-CLIP	26701625

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000086	Process	G2/M transition of mitotic cell cycle	TAS
GO:0000139	Component	Golgi membrane	IEA
GO:0001934	Process	Positive regulation of protein phosphorylation	IMP	20412773
GO:0004672	Function	Protein kinase activity	IDA	16618118
GO:0004672	Function	Protein kinase activity	ISS
GO:0004672	Function	Protein kinase activity	TAS	8786104
GO:0004674	Function	Protein serine/threonine kinase activity	IBA	21873635
GO:0004674	Function	Protein serine/threonine kinase activity	IDA	25500533
GO:0004674	Function	Protein serine/threonine kinase activity	TAS
GO:0005515	Function	Protein binding	IPI	16189514, 16618118, 20708156, 21179498, 22609948, 25416956, 32296183, 32814053
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	ISS
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005794	Component	Golgi apparatus	IDA	10826492
GO:0005813	Component	Centrosome	IDA	21399614, 21422228
GO:0005819	Component	Spindle	IDA	10826492
GO:0005829	Component	Cytosol	TAS
GO:0005876	Component	Spindle microtubule	IBA	21873635
GO:0005876	Component	Spindle microtubule	IDA	10826492
GO:0005886	Component	Plasma membrane	IDA	16027726
GO:0006468	Process	Protein phosphorylation	IDA	16618118
GO:0006468	Process	Protein phosphorylation	ISS
GO:0007020	Process	Microtubule nucleation	IMP	24648492
GO:0007030	Process	Golgi organization	IMP	24648492
GO:0010389	Process	Regulation of G2/M transition of mitotic cell cycle	TAS
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0018105	Process	Peptidyl-serine phosphorylation	IBA	21873635
GO:0018105	Process	Peptidyl-serine phosphorylation	IDA	25500533
GO:0032436	Process	Positive regulation of proteasomal ubiquitin-dependent protein catabolic process	IBA	21873635
GO:0032436	Process	Positive regulation of proteasomal ubiquitin-dependent protein catabolic process	ISS
GO:0032922	Process	Circadian regulation of gene expression	ISS
GO:0033116	Component	Endoplasmic reticulum-Golgi intermediate compartment membrane	TAS
GO:0034067	Process	Protein localization to Golgi apparatus	IMP	24648492
GO:0036064	Component	Ciliary basal body	IDA	29257953
GO:0042752	Process	Regulation of circadian rhythm	IBA	21873635
GO:0042752	Process	Regulation of circadian rhythm	ISS
GO:0045296	Function	Cadherin binding	HDA	25468996
GO:0048208	Process	COPII vesicle coating	TAS
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	16027726
GO:0050321	Function	Tau-protein kinase activity	IEA
GO:0051225	Process	Spindle assembly	IBA	21873635
GO:0051225	Process	Spindle assembly	IDA	10826492
GO:0061512	Process	Protein localization to cilium	IMP	24648492
GO:0071539	Process	Protein localization to centrosome	IMP	24648492
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IBA	21873635
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IMP	20412773
GO:0097711	Process	Ciliary basal body-plasma membrane docking	TAS
GO:0106310	Function	Protein serine kinase activity	IEA
GO:0106311	Function	Protein threonine kinase activity	IEA
GO:1905426	Process	Positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation	IC
GO:1905515	Process	Non-motile cilium assembly	IBA	21873635
GO:1905515	Process	Non-motile cilium assembly	IMP	24648492
GO:2000052	Process	Positive regulation of non-canonical Wnt signaling pathway	ISS

Other IDs

• MIM: 600864
• HGNC: 2452
• e!Ensembl: ENSG00000141551

Protein

• UniProt ID: P48730
• Protein name: Casein kinase I isoform delta (CKI-delta) (CKId) (EC 2.7.11.1) (Tau-protein kinase CSNK1D) (EC 2.7.11.26)
• Protein 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.
• PDB: 3UYS, 3UYT, 3UZP, 4HGT, 4HNF, 4KB8, 4KBA, 4KBC, 4KBK, 4TN6, 4TW9, 4TWC, 5IH4, 5IH5, 5IH6, 5MQV, 5OKT, 5W4W, 6F1W, 6F26, 6GZM, 6HMP, 6HMR, 6PXN, 6PXO, 6PXP, 6RCG, 6RCH, 6RU6, 6RU7, 6RU8
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00069	Pkinase	9 → 271	Protein kinase domain	Domain

• Sequence:

  MELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQ
  GGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIH
  SKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYA
  SINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVL
  CKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASRA
  ADDAERERRDREERLRHSRNPATRGLPSTASGRLRGTQEVAPPTPLTPTSHTANTSPRPV
  SGMERERKVSMRLHRGAPVNISSSDLTGRQDTSRMSTSQIPGRVASSGLQSVVHR

• Sequence length: 415

Pathways

KEGG:

Hedgehog signaling pathway
Hippo signaling pathway
Gap junction
Circadian rhythm

Reactome:

COPII-mediated vesicle transport
Regulation of PLK1 Activity at G2/M Transition
Loss of Nlp from mitotic centrosomes
Recruitment of mitotic centrosome proteins and complexes
Loss of proteins required for interphase microtubule organization from the centrosome
Recruitment of NuMA to mitotic centrosomes
Anchoring of the basal body to the plasma membrane
Major pathway of rRNA processing in the nucleolus and cytosol
AURKA Activation by TPX2

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Breast cancer	Malignant neoplasm of breast	rs587776547, rs1137887, rs137853007, rs587776650, rs80359351, rs80359714, rs121917783, rs104886456, rs121964878, rs80359874, rs80357868, rs80357508, rs387906843, rs80357569, rs80358158, rs80357524, rs80357115, rs80357945, rs80357729, rs80357609, rs80357259, rs80357981, rs80358063, rs80357389, rs80356862, rs80359876, rs80357580, rs80358053, rs80358089, rs80187739, rs397507241, rs80358069, rs80357590, rs80357284, rs80357941, rs80359261, rs80359272, rs80359276, rs276174813, rs80358474, rs80359316, rs1555282969, rs80359388, rs80359499, rs80359505, rs80359520, rs80359526, rs80359533, rs56253082, rs80358824, rs80359554, rs80359636, rs80359651, rs80359659, rs80359011, rs80359012, rs80359013, rs80359718, rs397507410, rs81002812, rs80359730, rs80359152, rs80359159, rs397507419, rs28897759, rs80359211, rs80359775, rs397514577, rs397507584, rs80358435, rs80358456, rs80359340, rs80359343, rs80359365, rs80358579, rs397507670, rs80358593, rs80359406, rs80359444, rs80359454, rs276174853, rs276174854, rs80359483, rs80359537, rs80358815, rs80358843, rs80359558, rs80359560, rs80359594, rs80358893, rs28897743, rs397507900, rs397507906, rs397507918, rs80358971, rs80358981, rs397507941, rs80359030, rs80359035, rs41293511, rs397507396, rs81002806, rs80359112, rs397508006, rs81002893, rs45580035, rs80359760, rs397508051, rs80359772, rs4987049, rs80359777, rs80357770, rs397508867, rs62625303, rs397508874, rs80357506, rs80357287, rs273898674, rs80358042, rs80358083, rs80357058, rs41286296, rs80357960, rs80356945, rs80357223, rs386134270, rs80358116, rs80357856, rs80357424, rs397509050, rs80357485, rs80357966, rs397509067, rs80357310, rs80356866, rs80357260, rs80357437, rs80358023, rs80358086, rs80357133, rs80356993, rs80357997, rs80357239, rs80357227, rs397509243, rs80356969, rs80356959, rs63750617, rs63751319, rs587779315, rs200640585, rs398122546, rs80357543, rs398122687, rs80359328, rs398122779, rs398122783, rs62517194, rs80358029, rs515726060, rs180177103, rs180177111, rs180177133, rs587776527, rs180177135, rs180177136, rs515726117, rs587779813, rs587779909, rs587780024, rs587780100, rs28909982, rs121908698, rs180177100, rs-1, rs587780210, rs587780240, rs587780639, rs587781269, rs587781353, rs587781471, rs587781658, rs587781697, rs587781730, rs587781894, rs587781948, rs587782005, rs587782011, rs200928781, rs587781558, rs370228071, rs587782245, rs587782401, rs180177110, rs587782504, rs72552322, rs587782531, rs587782620, rs587782680, rs587782774, rs587782818, rs730881411, rs730881389, rs564652222, rs397507768, rs587776419, rs730881868, rs730881940, rs56383036, rs758972589, rs201089102, rs730881348, rs786202608, rs786201886, rs786203318, rs786203775, rs786203714, rs786202033, rs750621215, rs786203884, rs786203650, rs772821016, rs863224521, rs864622223, rs864622655, rs375699023, rs876659572, rs768362387, rs876659535, rs876658957, rs483353072, rs876659435, rs267608041, rs876661113, rs730881369, rs878853535, rs772228129, rs878855122, rs760551339, rs80359596, rs397509222, rs886039630, rs886039683, rs886040828, rs587781799, rs886040374, rs886040649, rs397507967, rs878854957, rs886040043, rs1057517589, rs1060502769, rs866380588, rs863224765, rs1064793243, rs747563556, rs1555074976, rs1064795885, rs753961188, rs1064794708, rs869312772, rs1064793887, rs1131690820, rs1135401928, rs1135401868, rs1135401859, rs1553370324, rs397507630, rs1555283160, rs1555283251, rs1555283262, rs1555283361, rs1555286298, rs1555288462, rs886040950, rs1555289566, rs776323117, rs80357123, rs1555579627, rs1555580697, rs80358054, rs1555593302, rs1328985852, rs763470424, rs1555139694, rs878854697, rs1555461217, rs1555461765, rs774684620, rs766416564, rs1554558613, rs1305740166, rs1555461460, rs1555461407, rs1555461586, rs1555567202, rs1555607022, rs1555069815, rs1442299125, rs1474786480, rs1555084947, rs1555457867, rs141087784, rs1482641121, rs1564830522, rs1565469955, rs1565503137, rs864622613, rs755263466, rs757679199, rs1593903166, rs1597801649, rs1603293306, rs879253880, rs80358754, rs1597062038, rs45494092, rs1603275367, rs887358871, rs1597091518, rs1966967065, rs1064793049, rs2082872908, rs2085078278, rs2072475243
Advanced sleep phase syndrome	Familial advanced sleep-phase syndrome, Advanced Sleep-Phase Syndrome, Familial	rs121908635, rs104894561, rs397514693, rs1559332542	15800623
Migraine	Migraine Disorders	rs794727411
Migraine with aura	Migraine with Aura	rs-1

Unknown
Disease name	Disease term	dbSNP ID	References
Common migraine	Common Migraine
Sleep phase syndrome	ADVANCED SLEEP PHASE SYNDROME, FAMILIAL, 2		15800623, 25660813, 23636092