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	GRIN1
Previous Symbol	NMDAR1
Symbol Alias	GluN1
Approved Name	glutamate receptor, ionotropic, N-methyl D-aspartate 1
Previous Name	N-methyl-D-aspartate receptor subunit NR1
Location	9q34.3
Position	chr9:137138390-137168762, 1
External Links	HGNC: 4584 Entrez Gene: 2902 Ensembl: ENSG00000176884 UCSC: uc004cln.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
Georgi, A., 2006	SNP: rs10747050, rs11146020, rs4880213, rs6293	Our results do not support an association of the GRIN1 gene with BD in the German population.	Negative	Comment on Study
Mundo, E.,2003	Haplotype: (GRIN1_1001G/C) - (GRIN1_19700A/G) - (GRIN1_6608A/G)() Other variant: GRIN1_exon6_19700A/G, GRIN1_intron11_6608A/G, GRIN1_promoter_1001G/C	If these results are replicated there could be important implications for the involvement of the GRIN1 in the pathogenesis of BP.	Positive	Comment on Study
Yosifova, A.,2009	SNP: rs11146020, rs1126442, rs2301363	Significant association of SNP in this gene with BD in our population was observed.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 75)

GO terms by PBA (count: 12)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007411	axon guidance	biological process	TAS	60
GO:0005234	extracellular-glutamate-gated ion channel activity	molecular function	IBA	12
GO:0022843	voltage-gated cation channel activity	molecular function	IEA	1
GO:0045211	postsynaptic membrane	cellular component	IBA; ISS	68
GO:0005509	calcium ion binding	molecular function	ISS	50
GO:0006812	cation transport	biological process	IDA[7685113]	8
GO:0007268	synaptic transmission	biological process	TAS	116
GO:0005516	calmodulin binding	molecular function	ISS	20
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0005887	integral component of plasma membrane	cellular component	IDA[7685113]	158
GO:0045202	synapse	cellular component	ISS	29
GO:0005262	calcium channel activity	molecular function	IDA[7685113]	9

GO terms by database search (count: 63)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0045471	response to ethanol	biological process	IDA[18445116]	24
GO:0005783	endoplasmic reticulum	cellular component	IEA	49
GO:0016594	glycine binding	molecular function	IDA[7685113]; IMP[17047094]	6
GO:0001967	suckling behavior	biological process	IEA	3
GO:0034765	regulation of ion transmembrane transport	biological process	IEA	16
GO:0017146	N-methyl-D-aspartate selective glutamate receptor complex	cellular component	IDA[10480938]	5
GO:0035176	social behavior	biological process	IEA	17
GO:0035249	synaptic transmission, glutamatergic	biological process	IBA	14
GO:0051963	regulation of synapse assembly	biological process	IEA	3
GO:0030425	dendrite	cellular component	IDA[10749211]	65
GO:0060992	response to fungicide	biological process	IEA	1
GO:0043065	positive regulation of apoptotic process	biological process	IEA	25
GO:0042391	regulation of membrane potential	biological process	IDA[17047094]	13
GO:0043576	regulation of respiratory gaseous exchange	biological process	IEA	2
GO:0016595	glutamate binding	molecular function	IDA[7685113]	6
GO:0021987	cerebral cortex development	biological process	IEA	9
GO:0030054	cell junction	cellular component	IEA	88
GO:0051262	protein tetramerization	biological process	IEA	2
GO:0007585	respiratory gaseous exchange	biological process	IEA	3
GO:0014069	postsynaptic density	cellular component	ISS	26
GO:0060179	male mating behavior	biological process	IEA	1
GO:0060134	prepulse inhibition	biological process	IEA	8
GO:0050770	regulation of axonogenesis	biological process	IEA	7
GO:0006874	cellular calcium ion homeostasis	biological process	IEA	16
GO:0043005	neuron projection	cellular component	ISS	38
GO:0042165	neurotransmitter binding	molecular function	ISS	2
GO:0070588	calcium ion transmembrane transport	biological process	IEA	24
GO:0097481	neuronal postsynaptic density	cellular component	IEA	6
GO:0043524	negative regulation of neuron apoptotic process	biological process	IEA	26
GO:0035235	ionotropic glutamate receptor signaling pathway	biological process	IBA; ISS	13
GO:0035254	glutamate receptor binding	molecular function	IEA	4
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	ISS	91
GO:0043195	terminal bouton	cellular component	ISS	17
GO:0019899	enzyme binding	molecular function	IEA	34
GO:0005515	protein binding	molecular function	IPI[11937501]	563
GO:0001975	response to amphetamine	biological process	IEA	19
GO:0048511	rhythmic process	biological process	IEA	7
GO:0046982	protein heterodimerization activity	molecular function	IEA	42
GO:0060076	excitatory synapse	cellular component	ISS	3
GO:0043197	dendritic spine	cellular component	ISS	21
GO:0071287	cellular response to manganese ion	biological process	IEA	3
GO:0048814	regulation of dendrite morphogenesis	biological process	IEA	4
GO:0004972	N-methyl-D-aspartate selective glutamate receptor activity	molecular function	IDA[7679115]	5
GO:0009986	cell surface	cellular component	ISS	40
GO:0007616	long-term memory	biological process	IEA	9
GO:0008021	synaptic vesicle	cellular component	ISS	13
GO:0043278	response to morphine	biological process	IEA	9
GO:0034220	ion transmembrane transport	biological process	IBA	50
GO:0055074	calcium ion homeostasis	biological process	ISS	4
GO:0001661	conditioned taste aversion	biological process	IEA	4
GO:0008355	olfactory learning	biological process	IEA	2
GO:0048169	regulation of long-term neuronal synaptic plasticity	biological process	IEA	8
GO:0043083	synaptic cleft	cellular component	ISS	1
GO:0019233	sensory perception of pain	biological process	IEA	15
GO:0032590	dendrite membrane	cellular component	IEA	3
GO:0008344	adult locomotory behavior	biological process	IEA	15
GO:0008542	visual learning	biological process	ISS	17
GO:0048013	ephrin receptor signaling pathway	biological process	TAS	11
GO:0051592	response to calcium ion	biological process	IEA	7
GO:0021586	pons maturation	biological process	IEA	1
GO:0018964	propylene metabolic process	biological process	ISS	1
GO:0060079	regulation of excitatory postsynaptic membrane potential	biological process	ISS	10
GO:2000463	positive regulation of excitatory postsynaptic membrane potential	biological process	ISS	6

Gene related KEGG pathways (count: 3)

KEGG pathways by PBA (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04720	Long-term potentiation	13
hsa04020	Calcium signaling pathway	53

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04080	Neuroactive ligand-receptor interaction	92

Gene related BioCarta pathways (count: 2)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
PDZsPathway	Synaptic Proteins at the Synaptic Junction	1
eponfkbPathway	Erythropoietin mediated neuroprotection through NF-kB	2

Gene related interactors from protein-protein interactions data in HPRD (count: 32)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
GRIN1	CTNNB1	NO	in vivo	10862698
GRIN1	NANOS1	NO	in vivo	10862698
GRIN1	TUBA4	NO	in vivo	10862698
GRIN1	EPHB4	YES	in vivo	11136979
GRIN1	RAP2A	NO	in vivo	10862698
GRIN1	FUS	NO	in vivo	10862698
GRIN1	RPS6KA3	NO	in vivo	10862698
GRIN1	HRAS	NO	in vivo	10862698
GRIN1	PLAT	NO	in vitro	15448144
GRIN1	DUSP4	NO	in vivo	10862698
GRIN1	DLG4	NO	in vitro;in vivo	12068077 , 9502803 , 11506858 , 14732708 , 15030493 , 9009191 , 16767099
GRIN1	PPP2R1A	NO	in vivo	10862698
GRIN1	CIT	YES	in vivo	10862698
GRIN1	AKAP9	NO	in vitro;in vivo;yeast 2-hybrid	9482789 , 10862698
GRIN1	EPHB2	NO	in vitro	11754835
GRIN1	SP3	NO	in vivo	14970236
GRIN1	ACTN2	NO	in vitro;in vivo;yeast 2-hybrid	9728925 , 9952395 , 9009191
GRIN1	TRAF3	NO	in vivo	10862698
GRIN1	MAP2K2	NO	in vivo	10862698
GRIN1	MAP2	NO	in vivo	10862698
GRIN1	DLGAP4	NO	in vivo	10862698
GRIN1	MYH9	NO	in vivo	10862698
GRIN1	CALM1	NO	in vitro;in vivo	9728925 , 8625412 , 12408866 , 9009191 , 9952395
GRIN1	CDH2	NO	in vivo	10862698
GRIN1	TJP1	NO	in vivo	10862698
GRIN1	HNRNPU	NO	in vivo	10862698
GRIN1	DNM1	NO	in vitro	10862698
GRIN1	PRKCG	NO	in vivo	10862698
GRIN1	CANX	NO	in vitro;in vivo	14732708 , 11506858
GRIN1	SPTAN1	NO	in vitro;in vivo	9670010 , 10862698
GRIN1	CAMK2A	YES	in vivo	10862698
GRIN1	PRKCB	NO	in vivo	10862698

Related other genetic factors

Gene related SNPs (count: 9)

Literature-origin SNPs (count: 6)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs4880213	chr9:137136549 - 137136549(1)	upstream_gene_variant	1(0/1/0)
rs2301363	chr9:137139979 - 137139979(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
rs1126442	chr9:137156924 - 137156924(1)	missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	1(0/1/0)
rs6293	chr9:137156786 - 137156786(1)	NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	1(0/1/0)
rs11146020	chr9:137138632 - 137138632(1)	5_prime_UTR_variant; upstream_gene_variant	2(1/1/0)
rs10747050	chr9:137161424 - 137161424(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; splice_region_variant; upstream_gene_variant	1(0/1/0)

LD-proxies (count: 3)

rs_ID	Location	Functional Annotation
rs2301364	chr9:137140083 - 137140083(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs11794201	chr9:137159684 - 137159684(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs12238250	chr9:137152230 - 137152230(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 3)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
GRIN1_promoter_1001G/C	point mutation	promoter	1 (1/0/0)
GRIN1_intron11_6608A/G	point mutation	intron11	1 (1/0/0)
GRIN1_exon6_19700A/G	point mutation	exon6	1 (0/1/0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 9	chr9:0-138394717	3 (0/3/0)
9q33.3-34.3	chr9:123100000-138394717	1 (0/1/0)
9q34	chr9:127500000-138394717	1 (0/0/1)

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

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 0)

Overlap with SZ from candidate gene intersection analysis (count: 13)

Reference	ID in SZGene	Result Category
12454527	208	Negative
12082569	208	Negative
12210277	208	Negative
19158809	208	Negative
11109007	208	Negative
16476413	208	Positive
15564900	208	Negative
17728671	208	Negative
15841096	208	Negative
12363394	208	Negative
18792810	208	Positive
12707933	208	Negative
12679240	208	Positive

Gene relationship with MDD

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Region: chr9:137138390..137168762 View in gBrowse