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	SLC1A4
Symbol Alias	SATT, ASCT1
Approved Name	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4
Name Alias	alanine/serine/cysteine/threonine transporter
Location	2p15-p13
Position	chr2:64988477-65023865, 1
External Links	HGNC: 10942 Entrez Gene: 6509 Ensembl: ENSG00000115902 UCSC: uc010yqa.2
No. of Studies	1 (Positive: 0; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Skowronek, M. H., 2006	SNP: rs1064512, rs2075209, rs3732062, rs759458 Other variant: SLC1A4-11	Our results do not support an association of the ASCT1 gene with BD or SCZ in the German population.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 38)

GO terms by PBA (count: 6)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016021	integral component of membrane	cellular component	NAS[8101838]	219
GO:0005887	integral component of plasma membrane	cellular component	IC[8910405]	158
GO:0005254	chloride channel activity	molecular function	IDA[8910405]	12
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0016020	membrane	cellular component	IDA[19946888]	137
GO:0006811	ion transport	biological process	TAS	18

GO terms by database search (count: 32)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0070062	extracellular vesicular exosome	cellular component	IDA[20458337]	176
GO:1902476	chloride transmembrane transport	biological process	IDA[8910405]	16
GO:0042470	melanosome	cellular component	IEA	15
GO:0015824	proline transport	biological process	IDA[14502423]	1
GO:0034590	L-hydroxyproline transmembrane transporter activity	molecular function	IDA[14502423]	1
GO:0015180	L-alanine transmembrane transporter activity	molecular function	IDA[8101838]	1
GO:0035249	synaptic transmission, glutamatergic	biological process	NAS[16897601]	14
GO:0005813	centrosome	cellular component	IDA	34
GO:1903146	regulation of mitochondrion degradation	biological process	IMP[22020285]	5
GO:0015195	L-threonine transmembrane transporter activity	molecular function	IDA[8340364]	1
GO:0005882	intermediate filament	cellular component	ISS	8
GO:0015184	L-cystine transmembrane transporter activity	molecular function	IDA[8101838]; IDA[8340364]	1
GO:0030425	dendrite	cellular component	IEA	65
GO:0035524	proline transmembrane transport	biological process	IDA[14502423]	1
GO:0017153	sodium:dicarboxylate symporter activity	molecular function	IEA	3
GO:0043025	neuronal cell body	cellular component	IEA	50
GO:0006821	chloride transport	biological process	IDA[8910405]	4
GO:0006868	glutamine transport	biological process	TAS[21757002]	1
GO:0055085	transmembrane transport	biological process	TAS	77
GO:0006835	dicarboxylic acid transport	biological process	IEA	1
GO:0015194	L-serine transmembrane transporter activity	molecular function	IDA[8101838]	2
GO:0015193	L-proline transmembrane transporter activity	molecular function	IDA[14502423]	1
GO:0015186	L-glutamine transmembrane transporter activity	molecular function	TAS[21757002]	1
GO:0050890	cognition	biological process	IMP[16897601]	11
GO:0015811	L-cystine transport	biological process	IDA[8101838]; IDA[8340364]	1
GO:0005815	microtubule organizing center	cellular component	IDA	10
GO:0015826	threonine transport	biological process	IDA[8340364]	1
GO:0006865	amino acid transport	biological process	TAS	1
GO:0034589	hydroxyproline transport	biological process	IDA[14502423]	1
GO:0015825	L-serine transport	biological process	IDA[8101838]	2
GO:0015808	L-alanine transport	biological process	IDA[8101838]	1
GO:0009986	cell surface	cellular component	IDA[19581412]	40

Gene related KEGG pathways (count: 0)

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
SLC1A4	ERVWE1	NO	in vitro;in vivo	12050356 , 16820059

Related other genetic factors

Gene related SNPs (count: 6)

Literature-origin SNPs (count: 4)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs2075209	chr2:65018989 - 65018989(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(0/1/0)
rs759458	chr2:65018231 - 65018231(1)	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs1064512	chr2:64989752 - 64989752(1)	intron_variant; missense_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs3732062	chr2:65001102 - 65001102(1)	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 2)

rs_ID	Literature-origin SNPs with LD	Location	Functional Annotation
rs11675218		chr2:64987896 - 64987896(1)	upstream_gene_variant
rs11682919		chr2:64983692 - 64983692(1)	upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 1)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
SLC1A4-11	microsatellite		1 (0/1/0)

Gene related regions (count: 7)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
2p16.1-q11.2	chr2:54700000-102100000	1 (1/0/0)
2p16.2-p11.2	chr2:52600000-91800000	1 (1/0/0)
2p13-16	chr2:47500000-71300000	1 (0/0/1)
2p14-13.3	chr2:63900000-71300000	1 (0/1/0)
2p14-2p13.2	chr2:63900000-73300000	1 (0/0/1)
Chr 2	chr2:0-242193529	3 (0/3/0)
2p22.2-p13.3	chr2:36300000-71300000	1 (1/0/0)

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
17106422	Our results do not support an association of the ASCT1 gene with BD or SCZ in the German population.	Negative

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

Reference	ID in SZGene	Result Category
17106422	285	Negative
18638388	285	Positive

Gene relationship with MDD

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Region: chr2:64988477..65023865 View in gBrowse