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	CHRNA5
Approved Name	cholinergic receptor, nicotinic, alpha 5 (neuronal)
Previous Name	cholinergic receptor, nicotinic, alpha polypeptide 5
Name Alias	acetylcholine receptor, nicotinic, alpha 5 (neuronal)
Location	15q24
Position	chr15:78565520-78595269, 1
External Links	HGNC: 1959 Entrez Gene: 1138 Ensembl: ENSG00000169684 UCSC: uc002bdy.3
No. of Studies	3 (Positive: 2; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 3)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Hartz, S. M.,2011	SNP: rs16969968, rs637137, rs684513	No significant associations were detected in BD patients.	Negative	Comment on Study
Shi, J., 2007	SNP: rs2036527, rs4275821, rs514743, rs615470, rs680244, rs684513, rs951266	rs514743 showed nominally significant transmission bias; no evidence of interaction among these 19 cholinergic genes by FITF analysis and FDR correction was found	Positive	Comment on Study
Jackson, K. J., 2013	SNP: rs951266, rs16969968	Variants in the 15q25 gene cluster are associated with risk for schizophrenia/bipolar illness, negative symptoms of schizophrenia, and influence CHRNA5 expression in the brain and peripheral blood mononuclear cells.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 14)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0045211	postsynaptic membrane	cellular component	IEA	68
GO:0006812	cation transport	biological process	NAS[1542648]; TAS[20438829]	8
GO:0007268	synaptic transmission	biological process	TAS[9009220]	116
GO:0005886	plasma membrane	cellular component	TAS	360

GO terms by database search (count: 10)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005892	acetylcholine-gated channel complex	cellular component	IC[1542648]	13
GO:0015276	ligand-gated ion channel activity	molecular function	TAS[20438829]	7
GO:0004889	acetylcholine-activated cation-selective channel activity	molecular function	NAS[1542648]; TAS[20438829]	13
GO:0098655	cation transmembrane transport	biological process	IEA; NAS[1542648]; TAS[20438829]	16
GO:0015464	acetylcholine receptor activity	molecular function	IDA[1542648]	10
GO:0007165	signal transduction	biological process	NAS[9009220]	136
GO:0035095	behavioral response to nicotine	biological process	IMP[18227835]	6
GO:0006810	transport	biological process	NAS[1542648]	47
GO:0030054	cell junction	cellular component	IEA	88
GO:0034220	ion transmembrane transport	biological process	TAS[20438829]	50

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 1)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CHRNA5	CHRNB4	YES	in vitro	9655874

Related other genetic factors

Gene related SNPs (count: 30)

Literature-origin SNPs (count: 10)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs637137	chr15:78581634 - 78581634(1)	intron_variant	1(0/1/0)
rs16969968	chr15:78590583 - 78590583(1)	downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	2(1/1/0)
rs578776	chr15:78596058 - 78596058(1)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs684513	chr15:78566058 - 78566058(1)	intron_variant	2(0/2/0)
rs2036527	chr15:78559273 - 78559273(1)		1(0/1/0)
rs4275821	chr15:78557199 - 78557199(1)	downstream_gene_variant	1(0/1/0)
rs615470	chr15:78593646 - 78593646(1)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs514743	chr15:78591885 - 78591885(1)	downstream_gene_variant; intron_variant; upstream_gene_variant	1(1/0/0)
rs951266	chr15:78586199 - 78586199(1)	downstream_gene_variant; intron_variant; upstream_gene_variant	2(1/1/0)
rs680244	chr15:78578946 - 78578946(1)	intron_variant; upstream_gene_variant	1(0/1/0)

LD-proxies (count: 20)

rs_ID	Location	Functional Annotation
rs518425	chr15:78591471 - 78591471(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs12910984	chr15:78599285 - 78599285(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs667282	chr15:78571130 - 78571130(1)	intron_variant
rs569207	chr15:78580777 - 78580777(1)	intron_variant; upstream_gene_variant
rs6495306	chr15:78573551 - 78573551(1)	intron_variant
rs588765	chr15:78573083 - 78573083(1)	intron_variant
rs495956	chr15:78577588 - 78577588(1)	intron_variant; upstream_gene_variant
rs601079	chr15:78577237 - 78577237(1)	intron_variant; upstream_gene_variant
rs692780	chr15:78584163 - 78584163(1)	downstream_gene_variant; intron_variant
rs621849	chr15:78580519 - 78580519(1)	intron_variant; upstream_gene_variant
rs481134	chr15:78585221 - 78585221(1)	downstream_gene_variant; intron_variant
rs11637635	chr15:78584808 - 78584808(1)	downstream_gene_variant; intron_variant
rs647041	chr15:78588139 - 78588139(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs555018	chr15:78586900 - 78586900(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs660652	chr15:78595490 - 78595490(1)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs17408276	chr15:78589276 - 78589276(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant
rs472054	chr15:78595652 - 78595652(1)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs6495307	chr15:78597979 - 78597979(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs17486278	chr15:78575140 - 78575140(1)	intron_variant
rs7180002	chr15:78581651 - 78581651(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)
15q25-26	chr15:78000000-101991189	1 (1/0/0)
15q24.1-25.2	chr15:72400000-84700000	1 (0/1/0)
Chr 15	chr15:0-101991189	2 (0/2/0)

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

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Description	Result Category
23196875	Variants in the 15q25 gene cluster are associated with risk for schizophrenia/bipolar illness, negative symptoms of schizophrenia, and influence CHRNA5 expression in the brain and peripheral blood mononuclear cells.	Positive

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

Reference	ID in SZGene	Result Category
19944766	890	Negative

Gene relationship with MDD

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Region: chr15:78565520..78595269 View in gBrowse