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	SLC1A2
Symbol Alias	GLT-1, EAAT2
Approved Name	solute carrier family 1 (glial high affinity glutamate transporter), member 2
Location	11p13-p12
Position	chr11:35251206-35420063, -1
External Links	HGNC: 10940 Entrez Gene: 6506 Ensembl: ENSG00000110436 UCSC: uc001mwd.3
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Fiorentino, A., 2014	SNP: rs77619780, rs11033118, rs145827578, rs56205617, rs199599866, rs147294857, rs3812779 Other variant: SLC1A2_Chr1:35441380_G/C, SLC1A2_Chr1:35440927_A/G, SLC1A2_Chr1:35440635_G/A, SLC1A2_Chr1:35440563_C/G, SLC1A2_Chr1:35344202_G/T, SLC1A2_Chr1:35339061_C/T, SLC1A2_Chr1:35282452_C/T, SLC1A2_Chr1:35279202_A/G	Combined analysis of the recurrent-case-only missense variants and of the case-only missense and 5-UTR variants showed nominal evidence for association with the combined diseases	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 24)

GO terms by PBA (count: 5)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0016021	integral component of membrane	cellular component	IEA	219
GO:0007268	synaptic transmission	biological process	TAS[7521911]	116
GO:0016020	membrane	cellular component	TAS[7521911]	137
GO:0006811	ion transport	biological process	TAS	18

GO terms by database search (count: 19)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0017153	sodium:dicarboxylate symporter activity	molecular function	IEA	3
GO:0046326	positive regulation of glucose import	biological process	IEA	7
GO:0030673	axolemma	cellular component	IEA	2
GO:0009611	response to wounding	biological process	IEA	9
GO:0007632	visual behavior	biological process	IEA	2
GO:0055085	transmembrane transport	biological process	TAS	77
GO:0051938	L-glutamate import	biological process	IDA[7521911]	3
GO:0030534	adult behavior	biological process	IEA	6
GO:0042493	response to drug	biological process	IEA	57
GO:0021537	telencephalon development	biological process	IEA	5
GO:0010259	multicellular organismal aging	biological process	IEA	4
GO:0035264	multicellular organism growth	biological process	IEA	9
GO:0089711	L-glutamate transmembrane transport	biological process	IDA[7521911]; IEA	2
GO:0005515	protein binding	molecular function	IPI[19527721]	563
GO:0005313	L-glutamate transmembrane transporter activity	molecular function	IDA[7521911]	2
GO:0043200	response to amino acid	biological process	IEA	6
GO:0070779	D-aspartate import	biological process	IDA[7521911]	2
GO:0031668	cellular response to extracellular stimulus	biological process	IEA	4
GO:0015501	glutamate:sodium symporter activity	molecular function	IEA	2

Gene related KEGG pathways (count: 1)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa05030	Amyotrophic lateral sclerosis (ALS)	5

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 1)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
SLC1A2	JUB	NO	in vitro;in vivo;yeast 2-hybrid	11860269

Related other genetic factors

Gene related SNPs (count: 16)

Literature-origin SNPs (count: 8)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs3812779	chr11:35254932 - 35254932(1)	3_prime_UTR_variant; intron_variant	1(0/1/0)
rs11033118	chr11:35419707 - 35419707(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs199599866	chr11:35317442 - 35317442(1)	missense_variant	1(0/1/0)
rs145827578	chr11:35418951 - 35418951(1)	intron_variant; missense_variant; splice_region_variant; upstream_gene_variant	1(0/1/0)
rs3818275	chr11:35287236 - 35287236(1)	downstream_gene_variant; intron_variant; upstream_gene_variant	1(1/0/0)
rs147294857	chr11:35258680 - 35258680(1)	3_prime_UTR_variant; downstream_gene_variant; intron_variant	1(0/1/0)
rs77619780	chr11:35419764 - 35419764(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs56205617	chr11:35322560 - 35322560(1)	intron_variant; splice_donor_variant	1(0/1/0)

LD-proxies (count: 8)

rs_ID	Location	Functional Annotation
rs1321677	chr11:35293991 - 35293991(1)	intron_variant
rs4756208	chr11:35298537 - 35298537(1)	intron_variant
rs2421765	chr11:35299458 - 35299458(1)	intron_variant
rs3847607	chr11:35300038 - 35300038(1)	intron_variant
rs7130385	chr11:35249214 - 35249214(1)	downstream_gene_variant
rs11033052	chr11:35288591 - 35288591(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs2273689	chr11:35301653 - 35301653(1)	downstream_gene_variant; intron_variant; splice_region_variant; upstream_gene_variant
rs3847609	chr11:35300202 - 35300202(1)	intron_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 23)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
SLC1A2_Chr11:35441311_G/A		Chr11:35441311	0 (0/0/0)
SLC1A2_Chr11:35441380_G/C		Chr11:35441380	0 (0/0/0)
SLC1A2_Chr11:35440927_A/G		Chr11:35440927	0 (0/0/0)
SLC1A2_Chr11:35441254_C/T		Chr11:35441254	0 (0/0/0)
SLC1A2_Chr11:35276479_C/T		Chr11:35276479	0 (0/0/0)
SLC1A2_Chr1:35441380_G/C	point mutation	Putative promoter	1 (0/1/0)
SLC1A2_Chr11:35279202_A/G		Chr11:35279202	0 (0/0/0)
SLC1A2_Chr11:35280227_C/T		Chr11:35280227	0 (0/0/0)
SLC1A2_Chr11:35282452_C/T		Chr11:35282452	0 (0/0/0)
SLC1A2_Chr1:35440563_C/G	point mutation	5'-UTR	1 (0/1/0)
SLC1A2_Chr11:35338989_G/A		Chr11:35338989	0 (0/0/0)
SLC1A2_Chr1:35344202_G/T	point mutation	Exonic p.(A20S) 5'-UTR	1 (0/1/0)
SLC1A2_Chr11:35339061_C/T		Chr11:35339061	0 (0/0/0)
SLC1A2_Chr1:35440927_A/G	point mutation	5'-UTR	1 (0/1/0)
SLC1A2_Chr11:35344107_G/A		Chr11:35344107	0 (0/0/0)
SLC1A2_Chr1:35440635_G/A	point mutation	5'-UTR	1 (0/1/0)
SLC1A2_Chr11:35344202_G/T		Chr11:35344202	0 (0/0/0)
SLC1A2_Chr1:35279202_A/G	point mutation	3'-UTR	1 (0/1/0)
SLC1A2_Chr11:35440498_G/A		Chr11:35440498	0 (0/0/0)
SLC1A2_Chr11:35440563_C/G		Chr11:35440563	0 (0/0/0)
SLC1A2_Chr1:35339061_C/T	point mutation	Exonic p.(A7V)	1 (0/1/0)
SLC1A2_Chr1:35282452_C/T	point mutation	Exonic p.(R572C)	1 (0/1/0)
SLC1A2_Chr11:35440635_G/A		Chr11:35440635	0 (0/0/0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 11	chr11:0-135086622	2 (0/2/0)
11q14.3-11q21	chr11:22000000-97400000	1 (0/0/1)
11p13-q13.3	chr11:31000000-70500000	1 (0/1/0)

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
25406999	These findings are exploratory in nature and await replication in larger cohorts, however, they provide intriguing evidence that potentially functional rare variants in the SLC1A2 gene may confer susceptibility to psychotic disorders.	Trend

Overlap with SZ from candidate gene intersection analysis (count: 2)

Reference	ID in SZGene	Result Category
15296513	108	Positive
19660525	108	Negative

Gene relationship with MDD

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

Overlap with MDD from candidate gene intersection analysis (count: 5)

Reference	Description	Category in MDD	Link in MK4MDD
23415275		Neg	SLC1A2
24652383	We found two datasets where the mRNA levels of GAD1 and SLC1A2 in subregions of the dlPFC were significantly and marginally lower in subjects with MDD (n = 15) than in controls (n = 15) (p = 0.045 and 0.057, respectively)	Neg	SLC1A2
16230605	Microarray analysis of specific areas of cerebral cortex from individuals who had suffered from major depressive disorder demonstrated significant down-regulation of SLC1A2 and SLC1A3, two key members of the glutamate/neutral amino acid transporter protein family, SLC1. Similarly, expression of L-glutamate-ammonia ligase, the enzyme that converts glutamate to nontoxic glutamine was significantly decreased.	Pos	SLC1A2
17938633	Selected differentially expressed genes in BA44 to BA47 (ANOVA and t-test P < 0.01, fold change 1.3t)	Pos	SLC1A2
20386568	The expression of this gene was altered in the locus coeruleus of MDD	Pos	SLC1A2

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Region: chr11:35251206..35420063 View in gBrowse