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	CHRNA3
Approved Name	cholinergic receptor, nicotinic, alpha 3 (neuronal)
Previous Name	cholinergic receptor, nicotinic, alpha polypeptide 3
Name Alias	acetylcholine receptor, nicotinic, alpha 3 (neuronal)
Location	15q24
Position	chr15:78593052-78621295, -1
External Links	HGNC: 1957 Entrez Gene: 1136 Ensembl: ENSG00000080644 UCSC: uc002bec.3
No. of Studies	3 (Positive: 1; Negative: 2; 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
Shi, J., 2007	SNP: rs11637630, rs6495309	no evidence of interaction among these 19 cholinergic genes was found by Allelic Association, Haploview Tests, FITF analysis and FDR correction	Negative	Comment on Study
Jackson, K. J., 2013	SNP: rs1051730, rs8040868	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
Hartz, S. M.,2011	SNP: rs1051730, rs3743078, rs578776	No significant associations were detected in BD patients.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 28)

GO terms by PBA (count: 6)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0045211	postsynaptic membrane	cellular component	IEA	68
GO:0006811	ion transport	biological process	NAS[8906617]	18
GO:0016021	integral component of membrane	cellular component	NAS[8906617]	219
GO:0007268	synaptic transmission	biological process	TAS	116
GO:0007399	nervous system development	biological process	IMP[11450844]	40

GO terms by database search (count: 22)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0034220	ion transmembrane transport	biological process	TAS[20438829]	50
GO:0060079	regulation of excitatory postsynaptic membrane potential	biological process	ISS	10
GO:0007171	activation of transmembrane receptor protein tyrosine kinase activity	biological process	ISS	5
GO:0060084	synaptic transmission involved in micturition	biological process	IMP[11450844]	3
GO:0014069	postsynaptic density	cellular component	ISS	26
GO:0005892	acetylcholine-gated channel complex	cellular component	IDA[8906617]	13
GO:0004889	acetylcholine-activated cation-selective channel activity	molecular function	IDA[8906617]; TAS[20438829]	13
GO:0042391	regulation of membrane potential	biological process	ISS	13
GO:0042166	acetylcholine binding	molecular function	IC[8906617]	9
GO:0007626	locomotory behavior	biological process	ISS	23
GO:0007165	signal transduction	biological process	IDA[8906617]	136
GO:0014056	regulation of acetylcholine secretion, neurotransmission	biological process	ISS	1
GO:0015464	acetylcholine receptor activity	molecular function	IDA[8906617]	10
GO:0030425	dendrite	cellular component	ISS	65
GO:0098655	cation transmembrane transport	biological process	IDA[8906617]; IEA; TAS[20438829]	16
GO:0035095	behavioral response to nicotine	biological process	IMP[18227835]	6
GO:0007271	synaptic transmission, cholinergic	biological process	ISS	14
GO:0006940	regulation of smooth muscle contraction	biological process	ISS	5
GO:0048814	regulation of dendrite morphogenesis	biological process	ISS	4
GO:0015276	ligand-gated ion channel activity	molecular function	TAS[20438829]	7
GO:0043025	neuronal cell body	cellular component	ISS	50
GO:0030054	cell junction	cellular component	IEA	88

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 2)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CHRNA3	CHRNB4	YES	in vitro	1725184 , 1689727
CHRNA3	UBQLN1	NO	in vivo;yeast 2-hybrid	16091357

Related other genetic factors

Gene related SNPs (count: 31)

Literature-origin SNPs (count: 10)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
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)
rs11637630	chr15:78607377 - 78607377(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
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)
rs3743078	chr15:78602417 - 78602417(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs8040868	chr15:78618839 - 78618839(1)	5_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	1(1/0/0)
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)
rs1948	chr15:78625057 - 78625057(1)	3_prime_UTR_variant; downstream_gene_variant; synonymous_variant; upstream_gene_variant	1(1/0/0)
rs6495309	chr15:78622903 - 78622903(1)	downstream_gene_variant; upstream_gene_variant	1(0/1/0)
rs1051730	chr15:78601997 - 78601997(1)	NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	2(0/2/0)

LD-proxies (count: 21)

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
rs8042374	chr15:78615690 - 78615690(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs4887069	chr15:78616728 - 78616728(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs6495308	chr15:78615314 - 78615314(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs8042059	chr15:78615517 - 78615517(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs938682	chr15:78604205 - 78604205(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs7177514	chr15:78615064 - 78615064(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs647041	chr15:78588139 - 78588139(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
rs12914385	chr15:78606381 - 78606381(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs6495307	chr15:78597979 - 78597979(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs3743077	chr15:78602554 - 78602554(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs2869546	chr15:78615003 - 78615003(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs3743075	chr15:78617110 - 78617110(1)	downstream_gene_variant; missense_variant; NMD_transcript_variant; synonymous_variant
rs3743074	chr15:78617138 - 78617138(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; splice_region_variant
rs3743073	chr15:78617197 - 78617197(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant
rs1317286	chr15:78603787 - 78603787(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs1878399	chr15:78619661 - 78619661(1)	downstream_gene_variant; 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)
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
20393456	947	Negative

Gene relationship with MDD

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Region: chr15:78593052..78621295 View in gBrowse