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	CACNA1S
Previous Symbol	HOKPP, MHS5, CACNL1A3
Symbol Alias	Cav1.1, hypoPP
Approved Name	calcium channel, voltage-dependent, L type, alpha 1S subunit
Location	1q32
Position	chr1:201039512-201112566, -1
External Links	HGNC: 1397 Entrez Gene: 779 Ensembl: ENSG00000081248 UCSC: uc001gvv.3
No. of Studies	1 (Positive: 0; Negative: 1; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Jan, W. C., 2014	SNP: rs16847674, rs4915476, rs12139527, rs3850625	No marker in this gene was found to the significant.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 25)

GO terms by PBA (count: 5)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005245	voltage-gated calcium channel activity	molecular function	IDA[9852570]	14
GO:0007411	axon guidance	biological process	TAS	60
GO:0006816	calcium ion transport	biological process	IDA[9852570]	14
GO:0005886	plasma membrane	cellular component	IDA[11206130]	360
GO:0005891	voltage-gated calcium channel complex	cellular component	IDA[9852570]	13

GO terms by database search (count: 20)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0034765	regulation of ion transmembrane transport	biological process	IEA	16
GO:0048741	skeletal muscle fiber development	biological process	IEA	1
GO:0007520	myoblast fusion	biological process	IEA	4
GO:0005737	cytoplasm	cellular component	IDA[11206130]	322
GO:0006941	striated muscle contraction	biological process	IEA	2
GO:0007528	neuromuscular junction development	biological process	IEA	8
GO:0070509	calcium ion import	biological process	IBA	7
GO:0006936	muscle contraction	biological process	IMP[17418573]	10
GO:0046872	metal ion binding	molecular function	IEA	115
GO:0030315	T-tubule	cellular component	IDA[17204937]	8
GO:0007029	endoplasmic reticulum organization	biological process	IEA	3
GO:0005515	protein binding	molecular function	IPI[25416956]	563
GO:0008331	high voltage-gated calcium channel activity	molecular function	IDA[9852570]	7
GO:0070588	calcium ion transmembrane transport	biological process	IEA	24
GO:0002074	extraocular skeletal muscle development	biological process	IEA	1
GO:0001501	skeletal system development	biological process	IEA	16
GO:0086010	membrane depolarization during action potential	biological process	IBA	9
GO:0016529	sarcoplasmic reticulum	cellular component	IEA	6
GO:0031674	I band	cellular component	IDA[11206130]	1
GO:0043501	skeletal muscle adaptation	biological process	IEA	1

Gene related KEGG pathways (count: 3)

KEGG pathways by PBA (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04020	Calcium signaling pathway	53
hsa04010	MAPK signaling pathway	39

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04912	GnRH signaling pathway	17

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 3)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CACNA1S	SRI	NO	in vitro	9668070
CACNA1S	RYR1	NO	in vivo	12496092 , 9199552
CACNA1S	RIMS2	NO	in vitro	14660679

Related other genetic factors

Gene related SNPs (count: 38)

Literature-origin SNPs (count: 4)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs3850625	chr1:201047168 - 201047168(1)	downstream_gene_variant; missense_variant	1(0/1/0)
rs16847674	chr1:201078007 - 201078007(1)	synonymous_variant	1(0/1/0)
rs4915476	chr1:201077934 - 201077934(1)	synonymous_variant	1(0/1/0)
rs12139527	chr1:201040054 - 201040054(1)	downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 34)

rs_ID	Location	Functional Annotation
rs3767512	chr1:201083155 - 201083155(1)	intron_variant; splice_region_variant
rs734881	chr1:201081156 - 201081156(1)	intron_variant
rs7539618	chr1:201081440 - 201081440(1)	intron_variant
rs734879	chr1:201080779 - 201080779(1)	intron_variant
rs942705	chr1:201080918 - 201080918(1)	intron_variant
rs6667959	chr1:201079485 - 201079485(1)	intron_variant
rs942706	chr1:201080308 - 201080308(1)	intron_variant
rs4915477	chr1:201077947 - 201077947(1)	synonymous_variant
rs11811602	chr1:201078760 - 201078760(1)	intron_variant
rs3820422	chr1:201076345 - 201076345(1)	intron_variant
rs10920107	chr1:201076398 - 201076398(1)	intron_variant
rs2296386	chr1:201073855 - 201073855(1)	intron_variant
rs10920106	chr1:201074188 - 201074188(1)	intron_variant
rs3767506	chr1:201073025 - 201073025(1)	intron_variant
rs3767507	chr1:201073140 - 201073140(1)	intron_variant
rs12029212	chr1:201052491 - 201052491(1)	intron_variant
rs3818873	chr1:201054308 - 201054308(1)	intron_variant
rs2279944	chr1:201043119 - 201043119(1)	downstream_gene_variant; intron_variant
rs2297905	chr1:201047518 - 201047518(1)	downstream_gene_variant; intron_variant; splice_region_variant
rs12132696	chr1:201035384 - 201035384(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs6427874	chr1:201036426 - 201036426(1)	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs12032370	chr1:201055821 - 201055821(1)	intron_variant
rs1998721	chr1:201075620 - 201075620(1)	intron_variant; splice_region_variant
rs3767508	chr1:201074969 - 201074969(1)	intron_variant
rs9427468	chr1:201073198 - 201073198(1)	intron_variant
rs2886329	chr1:201072352 - 201072352(1)	intron_variant
rs9427711	chr1:201071052 - 201071052(1)	intron_variant
rs12409138	chr1:201098656 - 201098656(1)	intron_variant
rs7534906	chr1:201097752 - 201097752(1)	intron_variant
rs6677721	chr1:201096874 - 201096874(1)	intron_variant
rs10159219	chr1:201090659 - 201090659(1)	intron_variant
rs3767511	chr1:201083071 - 201083071(1)	intron_variant
rs4915213	chr1:201078646 - 201078646(1)	intron_variant
rs6672094	chr1:201077260 - 201077260(1)	intron_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)
1q32.1	chr1:198700000-207100000	2 (1/0/1)
1q31-q32	chr1:185800000-214400000	1 (0/1/0)
Chr 1	chr1:0-248956422	2 (0/2/0)

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

Gene relationship with SZ

Gene relationship with MDD

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Region: chr1:201039512..201112566 View in gBrowse