ADHDgene Database

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Large-scale studies

Data Summary

Published Variant
- SNP: 1391
- CNV: 398
- Others: 173
Published Gene: 359
Published Region: 128
Pathway by PBA: 8
Study: 361

Detail ...

Gene Report

Basic Info

Approved Symbol	SLC1A3
Symbol Alias	EAAT1, GLAST, EA6
Approved Name	solute carrier family 1 (glial high affinity glutamate transporter), member 3
Name Alias	glutamate transporter variant EAAT1ex9skip
Location	5p13
Position	chr5:36606457-36688436, +
External Links	HGNC: 10941 Entrez Gene: 6507 Ensembl: ENSG00000079215 UCSC: uc003jkj.3
No. of Studies	2 (significant: 1; non-significant: 1; trend: 0)
Source	Literature-origin; Mapped by LD-proxy; Mapped by literature SNP; Mapped by significant region

Gene related studies (count: 2)

Reference	Statistical Values/Author Comments	Result of Statistical Analysis
Turic D, 2005(a)	two marker haplotype (rs3776581/rs2269272) TRANSMIT P-value=0.016, X²(df=3)=10.47; two marker haplotype (rs2269272/rs2032893) TRANSMIT P-value=0.013, X²(df=3)=11.60; Haplotype T/G of rs2269272/rs2032893 P-value=0.003, X²(df=1)=9.43; genetic variation in SLC1A3 may contribute to susceptibility to ADHD	Significant
Laurin N, 2008(a)	single marker and haplotype analyses yielded little evidence for significant association	Non-significant

Gene related SNPs (count: 72)

Literature-origin SNPs (count: 23)

rs_ID	Location	Functional Annotation	No. of Studies (significant/non-significant/trend)
rs3733812	Chr5:36681521(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant	1(0/1/0)
rs1428975	Chr5:36623740(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)
rs4869686	Chr5:36679018(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1(0/1/0)
rs3776581	Chr5:36661944(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant	2(0/2/0)
rs3776585	Chr5:36668022(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant	1(0/1/0)
rs3776576	Chr5:36649627(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)
rs3776579	Chr5:36654493(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)
rs3776568	Chr5:36632611(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant	1(0/1/0)
rs930072	Chr5:36666071(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1(0/1/0)
rs2032892	Chr5:36677083(Fwd)	intron_variant; missense_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	1(0/1/0)
rs2032893	Chr5:36698622(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant	2(0/2/0)
rs1541815	Chr5:36702290(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant	1(0/1/0)
rs1049522	Chr5:36686886(Fwd)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1(0/1/0)
rs1049524	Chr5:36687393(Fwd)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1(0/1/0)
rs36684	Chr5:36699827(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant	1(0/1/0)
rs2301064	Chr5:36675699(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1(0/1/0)
rs1862638	Chr5:36628597(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)
rs4591778	Chr5:36608165(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant	1(0/1/0)
rs4421131	Chr5:36685465(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)
rs2269273	Chr5:36688098(Fwd)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1(0/1/0)
rs2269272	Chr5:36687856(Fwd)	3_prime_UTR_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	2(1/1/0)
rs2731886	Chr5:36606009(Fwd)	upstream_gene_variant	1(0/1/0)
rs3903407	Chr5:36656953(Fwd)	intron_variant; nc_transcript_variant	1(0/1/0)

LD-proxies (count: 49)

rs_ID	Location	Functional Annotation
rs1428967	Chr5:36646915(Fwd)	intron_variant; nc_transcript_variant
rs3776565	Chr5:36631653(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs16903247	Chr5:36653455(Fwd)	intron_variant; nc_transcript_variant
rs1622132	Chr5:36650706(Fwd)	intron_variant; nc_transcript_variant
rs4869683	Chr5:36658856(Fwd)	intron_variant; nc_transcript_variant
rs372171	Chr5:36636955(Fwd)	intron_variant; nc_transcript_variant
rs4869682	Chr5:36656718(Fwd)	intron_variant; nc_transcript_variant
rs1428968	Chr5:36646946(Fwd)	intron_variant; nc_transcript_variant
rs3822469	Chr5:36645367(Fwd)	intron_variant; nc_transcript_variant
rs3776573	Chr5:36646194(Fwd)	intron_variant; nc_transcript_variant
rs1030239	Chr5:36629258(Fwd)	intron_variant; nc_transcript_variant
rs3733810	Chr5:36631491(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs442867	Chr5:36635692(Fwd)	intron_variant; nc_transcript_variant
rs432268	Chr5:36636816(Fwd)	intron_variant; nc_transcript_variant
rs3776566	Chr5:36631733(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs3776567	Chr5:36632475(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs6451304	Chr5:36618403(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs10491374	Chr5:36667579(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant
rs3776578	Chr5:36651986(Fwd)	intron_variant; nc_transcript_variant
rs3776577	Chr5:36651105(Fwd)	intron_variant; nc_transcript_variant
rs1971720	Chr5:36663651(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs4869685	Chr5:36659084(Fwd)	intron_variant; nc_transcript_variant
rs3753180	Chr5:36672946(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs3756468	Chr5:36662889(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs1001571	Chr5:36671832(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs6892871	Chr5:36669569(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant
rs2301066	Chr5:36678275(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant
rs2301065	Chr5:36676567(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant
rs2301068	Chr5:36678540(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant
rs2301067	Chr5:36678453(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant
rs13436644	Chr5:36608101(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant
rs2731884	Chr5:36604214(Fwd)	upstream_gene_variant
rs2562580	Chr5:36604201(Fwd)	upstream_gene_variant
rs10078147	Chr5:36607962(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant
rs2562581	Chr5:36605100(Fwd)	upstream_gene_variant
rs2562577	Chr5:36603350(Fwd)	upstream_gene_variant
rs2562576	Chr5:36603290(Fwd)	upstream_gene_variant
rs1549627	Chr5:36676161(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant
rs2731883	Chr5:36604084(Fwd)	upstream_gene_variant
rs1423677	Chr5:36676523(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant
rs2562578	Chr5:36603375(Fwd)	upstream_gene_variant
rs3776586	Chr5:36684550(Fwd)	intron_variant; nc_transcript_variant
rs10080178	Chr5:36677792(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant
rs2731878	Chr5:36602563(Fwd)	upstream_gene_variant
rs4869487	Chr5:36692112(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs2562575	Chr5:36603226(Fwd)	upstream_gene_variant
rs2731879	Chr5:36602824(Fwd)	upstream_gene_variant
rs2033224	Chr5:36674079(Fwd)	downstream_gene_variant; intron_variant; nc_transcript_variant
rs7712125	Chr5:36669854(Fwd)	intron_variant; nc_transcript_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variant (count: 0)

Gene related regions (count: 1)

Region Name	Position	No. of Studies (significant/non-significant/trend)
5p13	chr5:28900000-42500000	3 (1/1/1)

Gene related GO terms (count: 29)

GO terms by PBA (with statistical significance of FDR<0.05) (count: 0)

GO terms by database search (count: 29)

ID	Name	Type	Evidence[PMID]	No. of Genes in ADHDgene
GO:0050806	positive regulation of synaptic transmission	Biological Process		2
GO:0050885	neuromuscular process controlling balance	Biological Process		8
GO:0051938	L-glutamate import	Biological Process	IDA[7521911]	1
GO:0055085	transmembrane transport	Biological Process		82
GO:0070779	D-aspartate import	Biological Process	IDA[7521911]	1
GO:0005314	high-affinity glutamate transmembrane transporter activity	Molecular Function		1
GO:0005886	plasma membrane	Cellular Component		772
GO:0001504	neurotransmitter uptake	Biological Process	TAS[8647279]	3
GO:0005313	L-glutamate transmembrane transporter activity	Molecular Function	TAS[7521911]	1
GO:0007268	synaptic transmission	Biological Process	TAS[7521911]	96
GO:0007605	sensory perception of sound	Biological Process		31
GO:0006537	glutamate biosynthetic process	Biological Process		2
GO:0006811	ion transport	Biological Process		25
GO:0042995	cell projection	Cellular Component		12
GO:0042493	response to drug	Biological Process		68
GO:0031223	auditory behavior	Biological Process		2
GO:0021545	cranial nerve development	Biological Process		1
GO:0048667	cell morphogenesis involved in neuron differentiation	Biological Process		2
GO:0046677	response to antibiotic	Biological Process		4
GO:0043205	fibril	Cellular Component		2
GO:0043025	neuronal cell body	Cellular Component		51
GO:0009986	cell surface	Cellular Component		70
GO:0009611	response to wounding	Biological Process		9
GO:0009449	gamma-aminobutyric acid biosynthetic process	Biological Process		1
GO:0009416	response to light stimulus	Biological Process		7
GO:0017153	sodium:dicarboxylate symporter activity	Molecular Function		1
GO:0016595	glutamate binding	Molecular Function		3
GO:0016021	integral to membrane	Cellular Component		845
GO:0016020	membrane	Cellular Component	TAS[7521911]	139

Gene related KEGG pathways (count: 1)

ID	Name	No. of Genes in ADHDgene	Brief Description
hsa04724	Glutamatergic synapse	43	Glutamate is the major excitatory neurotransmitter in the ma...... Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system(CNS). Glutamate is packaged into synaptic vesicles in the presynaptic terminal. Once released into the synaptic cleft, glutamate acts on postsynaptic ionotropic glutamate receptors (iGluRs) to mediate fast excitatory synaptic transmission. Glutamate can also act on metabotropic glutamate receptors (mGluRs) and exert a variety of modulatory effects through their coupling to G proteins and the subsequent recruitment of second messenger systems. Presynaptically localized Group II and Group III mGluRs are thought to represent the classical inhibitory autoreceptor mechanism that suppresses excess glutamate release. After its action on these receptors, glutamate can be removed from the synaptic cleft by EAATs located either on the presynaptic terminal, neighboring glial cells, or the postsynaptic neuron. In glia, glutamate is converted to glutamine, which is then transported back to the presynaptic terminal and converted back to glutamate. More...

Genes shared at least 5 GO terms with SLC1A3 (count: 13)

Gene Symbol	Pathway Count	Pathway List
SLC6A1	6	transmembrane transport; plasma membrane; synaptic transmission; cell surface; integral to membrane; membrane;
SLC6A3	6	transmembrane transport; plasma membrane; synaptic transmission; response to drug; neuronal cell body; integral to membrane;
CHRNA4	6	plasma membrane; synaptic transmission; ion transport; neuronal cell body; integral to membrane; membrane;
ADCY4	5	transmembrane transport; plasma membrane; synaptic transmission; integral to membrane; membrane;
GABRG3	5	transmembrane transport; plasma membrane; synaptic transmission; response to drug; integral to membrane;
SLC18A2	5	transmembrane transport; plasma membrane; synaptic transmission; neuronal cell body; membrane;
SLC3A2	5	transmembrane transport; plasma membrane; ion transport; cell surface; integral to membrane;
SLC4A2	5	transmembrane transport; plasma membrane; ion transport; integral to membrane; membrane;
SLC5A7	5	transmembrane transport; plasma membrane; synaptic transmission; neuronal cell body; integral to membrane;
ACHE	5	plasma membrane; synaptic transmission; cell surface; response to wounding; membrane;
CHRNA3	5	plasma membrane; synaptic transmission; ion transport; neuronal cell body; integral to membrane;
GRIN2A	5	plasma membrane; synaptic transmission; response to drug; cell surface; response to wounding;
GRM7	5	plasma membrane; synaptic transmission; sensory perception of sound; glutamate binding; integral to membrane;

Genes shared at least 2 KEGG pathways with SLC1A3 (count: 0)

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Region: chr5:36606457..36688436 View in gBrowse