BDgene

Core Gene from Gene Prioritization Pathways from PBA (Pathway-based Analysis) Enriched Pathways for Core Genes Enriched Pathways for Cross-disorder Genes

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Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	CSNK1D
Symbol Alias	HCKID, CKID, CKIdelta
Approved Name	casein kinase 1, delta
Location	17q25
Position	chr17:82239023-82273731, -1
External Links	HGNC: 2452 Entrez Gene: 1453 Ensembl: ENSG00000141551 UCSC: uc002kej.3
No. of Studies	4 (Positive: 2; Negative: 2; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 4)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Matsunaga, S.,2012	SNP: rs3829773, rs4789846, rs6502097, rs9901910	None of the SNPs showed a significant association with MDD, but a SNP (rs2075984) in CSNK1E and SNP (rs6502097) in CSNK1D were associated with SCZ (P=0.0091, uncorrected) and BD (P=0.030, uncorrected), respectively.	Positive	Comment on Study
Byrne, E. M., 2014		P-value=0.60. Gene-based tests show no significant association between this gene and BD.	Negative	Comment on Study
Kripke, D. F.,2009	SNP: rs4510078	Significant association was observed in the BP group.	Positive	Comment on Study
Mansour, H. A.,2009		Gene-based tests:X<sup>2</sup>=3.077, P-value = 0.125 in recessive model, X<sup>2</sup>=0.286, P-value = 0.613 in additive model, X<sup>2</sup>=0.001, P-value = 1 in dominant model in BPI. No significant association was observed using neither single SNP-based analyses nor gene-based tests in BPI.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 32)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005634	nucleus	cellular component	IBA; ISS	283
GO:0004672	protein kinase activity	molecular function	IDA[16618118]; ISS; TAS[8786104]	13
GO:0005886	plasma membrane	cellular component	IDA[16027726]	360
GO:0004674	protein serine/threonine kinase activity	molecular function	IBA	27

GO terms by database search (count: 28)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005794	Golgi apparatus	cellular component	IDA[10826492]	60
GO:0042277	peptide binding	molecular function	IEA	11
GO:0005813	centrosome	cellular component	IDA[21399614]	34
GO:0016055	Wnt signaling pathway	biological process	IEA	12
GO:0005524	ATP binding	molecular function	IEA	118
GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	biological process	ISS	7
GO:0008360	regulation of cell shape	biological process	IBA	16
GO:0051219	phosphoprotein binding	molecular function	IEA	3
GO:0001934	positive regulation of protein phosphorylation	biological process	IMP[20412773]	15
GO:0006996	organelle organization	biological process	TAS	23
GO:0007165	signal transduction	biological process	TAS[8786104]	136
GO:0005819	spindle	cellular component	IDA[10826492]	9
GO:0048471	perinuclear region of cytoplasm	cellular component	IDA[16027726]	50
GO:0042752	regulation of circadian rhythm	biological process	ISS	12
GO:0000086	G2/M transition of mitotic cell cycle	biological process	TAS	15
GO:0050321	tau-protein kinase activity	molecular function	IEA	2
GO:0018105	peptidyl-serine phosphorylation	biological process	IBA	11
GO:0005829	cytosol	cellular component	TAS	223
GO:0006897	endocytosis	biological process	IBA	15
GO:0051225	spindle assembly	biological process	IDA[10826492]	3
GO:0090263	positive regulation of canonical Wnt signaling pathway	biological process	IMP[20412773]	9
GO:0005876	spindle microtubule	cellular component	IDA[10826492]	2
GO:0032922	circadian regulation of gene expression	biological process	ISS	22
GO:0001948	glycoprotein binding	molecular function	IEA	4
GO:0006281	DNA repair	biological process	TAS[8786104]	16
GO:0000278	mitotic cell cycle	biological process	TAS	33
GO:0005515	protein binding	molecular function	IPI[16189514]	563
GO:0006468	protein phosphorylation	biological process	IDA[16618118]	42

Gene related KEGG pathways (count: 3)

KEGG pathways by PBA (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04540	Gap junction	15

KEGG pathways by database search (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04710	Circadian rhythm	11
hsa04340	Hedgehog signaling pathway	8

Gene related BioCarta pathways (count: 4)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 4)

ID	Name	No. of Genes in BDgene
p35alzheimersPathway	Deregulation of CDK5 in Alzheimers Disease	2
p53hypoxiaPathway	Hypoxia and p53 in the Cardiovascular system	6
wntPathway	WNT Signaling Pathway	5
ck1Pathway	Regulation of ck1/cdk5 by type 1 glutamate receptors	6

Gene related interactors from protein-protein interactions data in HPRD (count: 14)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CSNK1D	BACE1	NO	in vitro;in vivo	11278841
CSNK1D	AKAP9	NO	in vitro;in vivo;yeast 2-hybrid	12270714
CSNK1D	DVL3	NO	yeast 2-hybrid	16189514
CSNK1D	SNAPIN	NO	in vitro;yeast 2-hybrid	17101137
CSNK1D	CTNNB1	NO	in vitro	12000790 , 11955436
CSNK1D	PPP1R14A	NO	in vitro	15003508
CSNK1D	ARFGAP1	NO	in vitro	12181329
CSNK1D	PER3	YES	in vivo	11865049
CSNK1D	TP53	NO	in vitro;in vivo	9349507 , 10606744
CSNK1D	DVL1	YES	in vitro;in vivo;yeast 2-hybrid	11818547
CSNK1D	PER2	YES	in vitro	15800623
CSNK1D	PSEN2	NO	in vitro;in vivo	9990034 , 9558331 , 8972483
CSNK1D	CDK5	NO	in vitro	10500146
CSNK1D	SNCA	NO	in vitro;in vivo	10617630 , 10852916

Related other genetic factors

Gene related SNPs (count: 6)

Literature-origin SNPs (count: 5)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs4789846	chr17:82267669 - 82267669(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs9901910	chr17:82240131 - 82240131(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1(0/1/0)
rs6502097	chr17:82328303 - 82328303(1)	5_prime_UTR_variant; intron_variant; NMD_transcript_variant	1(1/0/0)
rs4510078	chr17:82247837 - 82247837(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs3829773	chr17:82263309 - 82263309(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 1)

rs_ID	Literature-origin SNPs with LD	Location	Functional Annotation
rs4239013		chr17:82270503 - 82270503(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
17q25	chr17:72900000-83257441	1 (0/0/1)
17q11-25	chr17:25100000-83257441	1 (1/0/0)
Chr 17	chr17:0-83257441	3 (0/3/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 3)

Reference	Description	Result Category
22981886	None of the SNPs showed a significant association with MDD, but a SNP (rs2075984) in CSNK1E and SNP (rs6502097) in CSNK1D were associated with SCZ (P=0.0091, uncorrected) and BD (P=0.030, uncorrected), respectively.	Negative
19839995	Gene-based tests:X<sup>2</sup>=2.253, P-value = 0.137 in additive model in SZ/SZA, X<sup>2</sup>=2.015, P-value = 0.173 in dominant model in SZ/SZA, X<sup>2</sup>=0.733, P-value = 0.425 in recessive model in SZ/SZA.No association was observed using neither single SNP-based analyses nor gene-based tests in SZ/SZA.	Negative
24687905	P-value=0.38. Gene-based tests show no significant association between this gene and SZ.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 1)

Reference	ID in SZGene	Result Category
19839995	879	Negative

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 2)

Reference	Description	Category in MDD
24687905	P-value=0.58. Gene-based tests show no significant association between this gene and MDD.	Negative
22981886	None of the SNPs showed a significant association with MDD, but a SNP (rs2075984) in CSNK1E and SNP (rs6502097) in CSNK1D were associated with SCZ (P=0.0091, uncorrected) and BD (P=0.030, uncorrected), respectively.	Negative

Overlap with MDD from candidate gene intersection analysis (count: 0)

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Region: chr17:82239023..82273731 View in gBrowse