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	CSNK1E
Symbol Alias	HCKIE, CKIE, CKIepsilon
Approved Name	casein kinase 1, epsilon
Location	22q13.1
Position	chr22:38290691-38398522, -1
External Links	HGNC: 2453 Entrez Gene: 1454 Ensembl: ENSG00000213923 UCSC: uc003avk.3
No. of Studies	5 (Positive: 1; Negative: 3; trend: 1)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 5)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Byrne, E. M., 2014		P-value=0.83. Gene-based tests show no significant association between this gene and BD.	Negative	Comment on Study
Mansour, H. A.,2009	SNP: rs1997644	Gene-based tests:X<sup>2</sup>=6.251, P-value = 0.098 in recessive model, X<sup>2</sup>=5.354, P-value = 0.14 in additive model, X<sup>2</sup>=3.728, P-value = 0.354 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
Soria, V.,2010	SNP: rs1997644	Significant associations of CSNK1E gene were found in BPD patients.	Positive	Comment on Study
Matsunaga, S.,2012	SNP: rs135745, rs135757, rs135764, rs1997644, rs2075984, rs3890379, rs6001093	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	Comment on Study
Nievergelt, C. M., 2006		Linkage analysis in 52 affected families showed suggestive evidence for linkage to CSNK1epsilon. This finding was not substantiated in the association study.	Trend	Comment on Study

Gene functional annotation

Gene related GO terms (count: 26)

GO terms by PBA (count: 3)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0004674	protein serine/threonine kinase activity	molecular function	IDA[15917222]; TAS[7797465]	27
GO:0004672	protein kinase activity	molecular function	ISS	13
GO:0005634	nucleus	cellular component	IBA; ISS	283

GO terms by database search (count: 23)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0030178	negative regulation of Wnt signaling pathway	biological process	IEA	5
GO:0005515	protein binding	molecular function	IPI[11425858]	563
GO:0006468	protein phosphorylation	biological process	IDA[15917222]; ISS	42
GO:0018105	peptidyl-serine phosphorylation	biological process	IBA	11
GO:0006897	endocytosis	biological process	IBA	15
GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	biological process	ISS	7
GO:0000086	G2/M transition of mitotic cell cycle	biological process	TAS	15
GO:0006996	organelle organization	biological process	TAS	23
GO:0090263	positive regulation of canonical Wnt signaling pathway	biological process	IEA	9
GO:0034613	cellular protein localization	biological process	IEA	4
GO:0005829	cytosol	cellular component	TAS	223
GO:0042752	regulation of circadian rhythm	biological process	ISS	12
GO:0000278	mitotic cell cycle	biological process	TAS	33
GO:0005737	cytoplasm	cellular component	IBA	322
GO:0030529	ribonucleoprotein complex	cellular component	IEA	4
GO:0032922	circadian regulation of gene expression	biological process	ISS	22
GO:0007623	circadian rhythm	biological process	TAS	40
GO:0016055	Wnt signaling pathway	biological process	IBA	12
GO:0005524	ATP binding	molecular function	IEA	118
GO:0044822	poly(A) RNA binding	molecular function	IDA[22681889]	44
GO:0007165	signal transduction	biological process	TAS[7797465]	136
GO:0008360	regulation of cell shape	biological process	IBA	16
GO:0006281	DNA repair	biological process	TAS[7797465]	16

Gene related KEGG pathways (count: 3)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 3)

ID	Name	No. of Genes in BDgene
hsa04710	Circadian rhythm	11
hsa04310	Wnt signaling pathway	20
hsa04340	Hedgehog signaling pathway	8

Gene related BioCarta pathways (count: 1)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
circadianPathway	Circadian Rhythms	6

Gene related interactors from protein-protein interactions data in HPRD (count: 18)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CSNK1E	AXIN2	NO	in vivo	12183362
CSNK1E	APC	NO	in vivo	11487578 , 15327768
CSNK1E	BID	NO	in vitro;in vivo	11583622
CSNK1E	AXIN1	NO	in vitro;in vivo;yeast 2-hybrid	11487578 , 12000790
CSNK1E	PER3	YES	in vitro;in vivo	10899319 , 11865049
CSNK1E	RAD54B	NO	yeast 2-hybrid	16189514
CSNK1E	DVL3	NO	in vivo	10535959
CSNK1E	AKAP9	NO	in vitro;yeast 2-hybrid	12270714
CSNK1E	OCLN	NO	in vivo;yeast 2-hybrid	16616143
CSNK1E	DVL1	YES	in vitro;in vivo	11487578 , 11818547
CSNK1E	PER2	YES	in vitro;in vivo	11232563 , 9349507 , 17218255
CSNK1E	ANKRD6	NO	in vivo;yeast 2-hybrid	12183362
CSNK1E	DVL2	NO	yeast 2-hybrid	16189514
CSNK1E	SOCS3	NO	in vitro;in vivo	15070676
CSNK1E	PPP1R14A	NO	in vitro	15003508
CSNK1E	ARNTL	YES	in vitro	11875063
CSNK1E	PER1	YES	in vitro;in vivo	10848614 , 11865049
CSNK1E	CRY1	YES	in vivo	11875063

Related other genetic factors

Gene related SNPs (count: 15)

Literature-origin SNPs (count: 7)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs1997644	chr22:38319217 - 38319217(1)	intron_variant; upstream_gene_variant	3(2/1/0)
rs135764	chr22:38314407 - 38314407(1)	intron_variant	1(0/1/0)
rs3890379	chr22:38296374 - 38296374(1)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1(0/1/0)
rs135745	chr22:38287631 - 38287631(1)	downstream_gene_variant	1(0/1/0)
rs6001093	chr22:38305388 - 38305388(1)	intron_variant; upstream_gene_variant	1(0/1/0)
rs2075984	chr22:38294883 - 38294883(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1(0/1/0)
rs135757	chr22:38307648 - 38307648(1)	intron_variant; upstream_gene_variant	1(0/1/0)

LD-proxies (count: 8)

rs_ID	Location	Functional Annotation
rs5750581	chr22:38299401 - 38299401(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs135756	chr22:38307584 - 38307584(1)	intron_variant; upstream_gene_variant
rs867198	chr22:38312601 - 38312601(1)	intron_variant
rs1534891	chr22:38299094 - 38299094(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs7284708	chr22:38307101 - 38307101(1)	intron_variant; upstream_gene_variant
rs1005473	chr22:38298367 - 38298367(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs2075983	chr22:38294692 - 38294692(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs135763	chr22:38312399 - 38312399(1)	intron_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 5)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
22q12.3-13.32	chr22:31800000-49100000	1 (0/1/0)
Chr 22	chr22:0-50818468	2 (0/1/1)
22q12.3-q13.33	chr22:31800000-50818468	1 (1/0/0)
22q13	chr22:37200000-50818468	1 (1/0/0)
22q13.1	chr22:37200000-40600000	1 (0/0/1)

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
24687905	P-value=0.20. The results from the gene-based test indicate that CSNK1E is the best candidates among the circadian genes to influence SCZ risk.	Negative
19839995	Gene-based tests:X<sup>2</sup>=3.815, P-value = 0.347 in dominant model in SZ/SZA, X<sup>2</sup>=2.768, P-value = 0.564 in recessive model in SZ/SZA, X<sup>2</sup>=1.423, P-value = 0.814 in additive model in SZ/SZA.No association was observed using neither single SNP-based analyses nor gene-based tests in SZ/SZA.	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.	Positive

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

Reference	ID in SZGene	Result Category
19839995	880	Negative

Gene relationship with MDD

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

Reference	Description	Category in MDD
20072116	No significant associations of CSNK1E gene were found in MDD patients.	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
24687905	P-value=0.80. Gene-based tests show no significant association between this gene and MDD.	Negative

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

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Region: chr22:38290691..38398522 View in gBrowse