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	CHRNA1
Previous Symbol	CHRNA
Approved Name	cholinergic receptor, nicotinic, alpha 1 (muscle)
Previous Name	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)
Name Alias	acetylcholine receptor, nicotinic, alpha 1 (muscle)
Location	2q31.1
Position	chr2:174747592-174787935, -1
External Links	HGNC: 1955 Entrez Gene: 1134 Ensembl: ENSG00000138435 UCSC: uc002uje.2
No. of Studies	2 (Positive: 0; Negative: 1; trend: 1)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 2)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Georgieva, L., 2014		A de novo CNV in this gene was detected in BD.	Trend	Comment on Study
Shi, J., 2007	SNP: rs3755486, rs6708544, rs6732758, rs935863	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

Gene functional annotation

Gene related GO terms (count: 25)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005216	ion channel activity	molecular function	TAS[6688857]	2
GO:0005886	plasma membrane	cellular component	ISS[8872460]; TAS	360
GO:0007268	synaptic transmission	biological process	TAS	116
GO:0045211	postsynaptic membrane	cellular component	NAS[18252226]	68

GO terms by database search (count: 21)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0004889	acetylcholine-activated cation-selective channel activity	molecular function	IMP[9221765]; ISS[8872460]	13
GO:0031594	neuromuscular junction	cellular component	IDA[9221765]; ISS[8872460]	9
GO:0070050	neuron cellular homeostasis	biological process	IMP[8872460]	2
GO:0019228	neuronal action potential	biological process	IMP[8872460]	11
GO:0015464	acetylcholine receptor activity	molecular function	ISS[8872460]	10
GO:0098655	cation transmembrane transport	biological process	IEA; IMP[9221765]; ISS[8872460]; TAS[7619526]	16
GO:0007528	neuromuscular junction development	biological process	IMP[9221765]	8
GO:0042391	regulation of membrane potential	biological process	IMP[8872460]	13
GO:0048630	skeletal muscle tissue growth	biological process	IMP[18252226]	1
GO:0007274	neuromuscular synaptic transmission	biological process	IMP[9221765]	5
GO:0005892	acetylcholine-gated channel complex	cellular component	ISS[8872460]	13
GO:0006810	transport	biological process	TAS[7619526]	47
GO:0042166	acetylcholine binding	molecular function	ISS[8872460]	9
GO:0046716	muscle cell cellular homeostasis	biological process	IMP[8872460]	4
GO:0030054	cell junction	cellular component	IEA	88
GO:0034220	ion transmembrane transport	biological process	TAS[6688857]	50
GO:0009986	cell surface	cellular component	IDA[12928480]	40
GO:0050881	musculoskeletal movement	biological process	IMP[18252226]	1
GO:0003009	skeletal muscle contraction	biological process	IMP[8872460]	4
GO:0007165	signal transduction	biological process	TAS[7619526]	136
GO:0050905	neuromuscular process	biological process	IMP[9546329]	3

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 3)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 3)

ID	Name	No. of Genes in BDgene
agrPathway	Agrin in Postsynaptic Differentiation	8
botulinPathway	Blockade of Neurotransmitter Relase by Botulinum Toxin	4
no1Pathway	Actions of Nitric Oxide in the Heart	9

Gene related interactors from protein-protein interactions data in HPRD (count: 4)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CHRNA1	CHRNE	NO	in vitro	1712080
CHRNA1	CHRNG	NO	in vitro	7695910
CHRNA1	CHRND	NO	in vitro	7695910 , 8910344
CHRNA1	ITGA7	NO	in vivo	10910772

Related other genetic factors

Gene related SNPs (count: 13)

Literature-origin SNPs (count: 4)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs6732758	chr2:174745231 - 174745231(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(0/1/0)
rs3755486	chr2:174767158 - 174767158(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs6708544	chr2:174739466 - 174739466(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs935863	chr2:174772073 - 174772073(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 9)

rs_ID	Location	Functional Annotation
rs1376865	chr2:174759869 - 174759869(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs2600683	chr2:174765747 - 174765747(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs12997022	chr2:174755246 - 174755246(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1530906	chr2:174756207 - 174756207(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs2646165	chr2:174756754 - 174756754(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7560774	chr2:174764293 - 174764293(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs3755485	chr2:174765825 - 174765825(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2600685	chr2:174762320 - 174762320(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs3816448	chr2:174748331 - 174748331(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant

Gene related CNVs (count: 1)

ID	Location	Size	Band	Type	Inheritance
CNV_Lyudmila Georgieva[2014]_1	chr2:175365518-175813657 (UCSC build 37, hg19)	448139	2q31.1	deletion

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
2q21-q33	chr2:129100000-208200000	1 (0/0/1)
Chr 2	chr2:0-242193529	3 (0/3/0)
2q24-33	chr2:154000000-208200000	1 (1/0/0)

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

Gene relationship with SZ

Gene relationship with MDD

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Region: chr2:174747592..174787935 View in gBrowse