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	CHRM3
Approved Name	cholinergic receptor, muscarinic 3
Name Alias	acetylcholine receptor, muscarinic 3
Location	1q43
Position	chr1:239386565-239915452, 1
External Links	HGNC: 1952 Entrez Gene: 1131 Ensembl: ENSG00000133019 UCSC: uc001hyp.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
Shi, J., 2007	SNP: rs1019882, rs10495447, rs528011, rs543307, rs621060, rs658842, rs6688537, rs6700643, rs7520974	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: 33)

GO terms by PBA (count: 6)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0045202	synapse	cellular component	IBA	29
GO:0005887	integral component of plasma membrane	cellular component	ISS	158
GO:0007399	nervous system development	biological process	TAS[2739737]	40
GO:0004872	receptor activity	molecular function	TAS[10940357]	19
GO:0045211	postsynaptic membrane	cellular component	IEA	68
GO:0005886	plasma membrane	cellular component	TAS	360

GO terms by database search (count: 27)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0043679	axon terminus	cellular component	IEA	8
GO:0032279	asymmetric synapse	cellular component	IEA	3
GO:0030054	cell junction	cellular component	IEA	88
GO:0046541	saliva secretion	biological process	IEA	2
GO:0007213	G-protein coupled acetylcholine receptor signaling pathway	biological process	ISS	6
GO:0045987	positive regulation of smooth muscle contraction	biological process	IEA	3
GO:0007197	adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway	biological process	IBA	5
GO:0007606	sensory perception of chemical stimulus	biological process	IBA	14
GO:0044281	small molecule metabolic process	biological process	TAS	117
GO:0006939	smooth muscle contraction	biological process	IEA	7
GO:0042166	acetylcholine binding	molecular function	ISS	9
GO:0007207	phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway	biological process	IBA	5
GO:0030425	dendrite	cellular component	IEA	65
GO:0004435	phosphatidylinositol phospholipase C activity	molecular function	TAS[1905013]	8
GO:0003056	regulation of vascular smooth muscle contraction	biological process	IBA	1
GO:0050796	regulation of insulin secretion	biological process	TAS	24
GO:0010579	positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway	biological process	IBA	16
GO:0005515	protein binding	molecular function	IPI[19575010]	563
GO:0006112	energy reserve metabolic process	biological process	TAS	19
GO:0007186	G-protein coupled receptor signaling pathway	biological process	TAS[9603968]	64
GO:0016323	basolateral plasma membrane	cellular component	IEA	21
GO:0016907	G-protein coupled acetylcholine receptor activity	molecular function	ISS	5
GO:0008283	cell proliferation	biological process	TAS[8063729]	37
GO:0008144	drug binding	molecular function	IEA	21
GO:0007165	signal transduction	biological process	TAS[10940357]	136
GO:0006464	cellular protein modification process	biological process	TAS[10051746]	7
GO:0007271	synaptic transmission, cholinergic	biological process	IBA	14

Gene related KEGG pathways (count: 3)

KEGG pathways by PBA (count: 1)

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

KEGG pathways by database search (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04080	Neuroactive ligand-receptor interaction	92
hsa04810	Regulation of actin cytoskeleton	24

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 8)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CHRM3	ARF6	NO	in vitro;in vivo	12799371
CHRM3	GZMB	NO	in vitro;in vivo	11665980
CHRM3	PPP1R9B	NO	in vitro	17464283
CHRM3	CSNK1A1	NO	in vitro	10777483
CHRM3	ARF1	NO	in vitro;in vivo	12799371
CHRM3	GRK6	NO	in vitro	11856737
CHRM3	GNAQ	NO	in vivo	7629074
CHRM3	GPRASP1	NO	in vitro	15452121

Related other genetic factors

Gene related SNPs (count: 84)

Literature-origin SNPs (count: 9)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs6700643	chr1:239635621 - 239635621(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs621060	chr1:239828986 - 239828986(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs10495447	chr1:239888040 - 239888040(1)	downstream_gene_variant; intron_variant	1(0/1/0)
rs658842	chr1:239785335 - 239785335(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs6688537	chr1:239687288 - 239687288(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs528011	chr1:239855007 - 239855007(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs7520974	chr1:239903960 - 239903960(1)	intron_variant; upstream_gene_variant	1(0/1/0)
rs543307	chr1:239764310 - 239764310(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs1019882	chr1:239735556 - 239735556(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 75)

rs_ID	Location	Functional Annotation
rs6429147	chr1:239631494 - 239631494(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs10925934	chr1:239635048 - 239635048(1)	intron_variant; non_coding_transcript_variant
rs1867263	chr1:239644620 - 239644620(1)	intron_variant; non_coding_transcript_variant
rs2120241	chr1:239645191 - 239645191(1)	intron_variant; non_coding_transcript_variant
rs10802785	chr1:239645729 - 239645729(1)	intron_variant; non_coding_transcript_variant
rs10925941	chr1:239649238 - 239649238(1)	intron_variant; non_coding_transcript_variant
rs1899616	chr1:239655268 - 239655268(1)	intron_variant; non_coding_transcript_variant
rs4659550	chr1:239656203 - 239656203(1)	intron_variant; non_coding_transcript_variant
rs12093821	chr1:239660948 - 239660948(1)	intron_variant; non_coding_transcript_variant
rs2165872	chr1:239663688 - 239663688(1)	intron_variant; non_coding_transcript_variant
rs16838637	chr1:239665050 - 239665050(1)	intron_variant; non_coding_transcript_variant
rs1899613	chr1:239672103 - 239672103(1)	intron_variant; non_coding_transcript_variant
rs10802813	chr1:239889304 - 239889304(1)	downstream_gene_variant; intron_variant
rs10802814	chr1:239890697 - 239890697(1)	downstream_gene_variant; intron_variant
rs10495448	chr1:239892173 - 239892173(1)	intron_variant
rs514050	chr1:239829783 - 239829783(1)	intron_variant; non_coding_transcript_variant
rs618713	chr1:239828495 - 239828495(1)	intron_variant; non_coding_transcript_variant
rs2841040	chr1:239799881 - 239799881(1)	intron_variant; non_coding_transcript_variant
rs665159	chr1:239798702 - 239798702(1)	intron_variant; non_coding_transcript_variant
rs619214	chr1:239795322 - 239795322(1)	intron_variant; non_coding_transcript_variant
rs10802811	chr1:239885352 - 239885352(1)	intron_variant; non_coding_transcript_variant
rs643040	chr1:239784120 - 239784120(1)	intron_variant; non_coding_transcript_variant
rs10802812	chr1:239889122 - 239889122(1)	downstream_gene_variant; intron_variant
rs12131198	chr1:239889149 - 239889149(1)	downstream_gene_variant; intron_variant
rs1155612	chr1:239734405 - 239734405(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2355210	chr1:239725457 - 239725457(1)	intron_variant; non_coding_transcript_variant
rs6657343	chr1:239728211 - 239728211(1)	intron_variant; non_coding_transcript_variant
rs717227	chr1:239719299 - 239719299(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs6694220	chr1:239720316 - 239720316(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs988231	chr1:239696190 - 239696190(1)	intron_variant; non_coding_transcript_variant
rs891700	chr1:239718626 - 239718626(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs12406493	chr1:239689805 - 239689805(1)	intron_variant; non_coding_transcript_variant
rs6429152	chr1:239690837 - 239690837(1)	intron_variant; non_coding_transcript_variant
rs6688548	chr1:239687338 - 239687338(1)	intron_variant; non_coding_transcript_variant
rs497576	chr1:239862677 - 239862677(1)	intron_variant; non_coding_transcript_variant
rs6669810	chr1:239905329 - 239905329(1)	intron_variant
rs12036109	chr1:239902578 - 239902578(1)	intron_variant; upstream_gene_variant
rs654209	chr1:239765617 - 239765617(1)	intron_variant; non_coding_transcript_variant
rs7513746	chr1:239699111 - 239699111(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs2841036	chr1:239763732 - 239763732(1)	intron_variant; non_coding_transcript_variant
rs2278642	chr1:239703843 - 239703843(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs2790328	chr1:239763515 - 239763515(1)	intron_variant; non_coding_transcript_variant
rs12751235	chr1:239706521 - 239706521(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs10802794	chr1:239707321 - 239707321(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant
rs10802795	chr1:239707475 - 239707475(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant
rs525389	chr1:239769082 - 239769082(1)	intron_variant; non_coding_transcript_variant
rs1134	chr1:239708872 - 239708872(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs532718	chr1:239768318 - 239768318(1)	intron_variant; non_coding_transcript_variant
rs3738436	chr1:239709193 - 239709193(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs479933	chr1:239766605 - 239766605(1)	intron_variant; non_coding_transcript_variant
rs6429154	chr1:239713966 - 239713966(1)	intron_variant; non_coding_transcript_variant
rs480000	chr1:239766577 - 239766577(1)	intron_variant; non_coding_transcript_variant
rs644326	chr1:239777828 - 239777828(1)	intron_variant; non_coding_transcript_variant
rs485412	chr1:239776596 - 239776596(1)	intron_variant; non_coding_transcript_variant
rs481036	chr1:239773282 - 239773282(1)	intron_variant; non_coding_transcript_variant
rs663927	chr1:239772051 - 239772051(1)	intron_variant; non_coding_transcript_variant
rs7552453	chr1:239693534 - 239693534(1)	intron_variant; non_coding_transcript_variant
rs2355237	chr1:239694224 - 239694224(1)	intron_variant; non_coding_transcript_variant
rs652349	chr1:239765167 - 239765167(1)	intron_variant; non_coding_transcript_variant
rs6429153	chr1:239695425 - 239695425(1)	intron_variant; non_coding_transcript_variant
rs1416789	chr1:239738345 - 239738345(1)	intron_variant; non_coding_transcript_variant
rs11579382	chr1:239737706 - 239737706(1)	intron_variant; non_coding_transcript_variant
rs10802801	chr1:239739541 - 239739541(1)	intron_variant; non_coding_transcript_variant
rs10925964	chr1:239739214 - 239739214(1)	intron_variant; non_coding_transcript_variant
rs10802802	chr1:239746642 - 239746642(1)	intron_variant; non_coding_transcript_variant
rs11585281	chr1:239746351 - 239746351(1)	intron_variant; non_coding_transcript_variant
rs12029701	chr1:239747301 - 239747301(1)	intron_variant; non_coding_transcript_variant
rs6663632	chr1:239714421 - 239714421(1)	intron_variant; non_coding_transcript_variant
rs6684622	chr1:239714237 - 239714237(1)	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs7511970	chr1:239719955 - 239719955(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs1431719	chr1:239717903 - 239717903(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs12743042	chr1:239725004 - 239725004(1)	intron_variant; non_coding_transcript_variant
rs1431721	chr1:239722510 - 239722510(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs1155611	chr1:239734527 - 239734527(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs6695600	chr1:239725087 - 239725087(1)	intron_variant; non_coding_transcript_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 1)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
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

View in gBrowse

Region: chr1:239386565..239915452 View in gBrowse