Gene Report

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Basic Info

Approved Symbol	SLC6A5
Previous Symbol	NET1
Symbol Alias	GLYT2
Approved Name	solute carrier family 6 (neurotransmitter transporter), member 5
Previous Name	solute carrier family 6 (neurotransmitter transporter, glycine), member 5
Name Alias	glycine transporter 2
Location	11p15.1
Position	chr11:20599400-20659285, 1
External Links	HGNC: 11051 Entrez Gene: 9152 Ensembl: ENSG00000165970 UCSC: uc001mqd.3
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
Jamra, R. A., 2006 (b)	SNP: rs1805091, rs2000959, rs2241940, rs2289683 Other variant: SLC6A5_AC-tandem-repeat	Our results do not suggest that a common genetic variant at the GLYT2 locus contributes to BPAD and/or schizophrenia in patients of German descent.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 10)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007268	synaptic transmission	biological process	TAS[9845349]	116
GO:0016021	integral component of membrane	cellular component	IEA	219
GO:0005886	plasma membrane	cellular component	IDA[16751771]; TAS	360

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005328	neurotransmitter:sodium symporter activity	molecular function	IEA	1
GO:0036233	glycine import	biological process	IDA[16751771]	1
GO:0055085	transmembrane transport	biological process	TAS	77
GO:0060012	synaptic transmission, glycinergic	biological process	IMP[16751771]	2
GO:0006836	neurotransmitter transport	biological process	IEA	5
GO:0015375	glycine:sodium symporter activity	molecular function	IDA[16751771]	1
GO:0006810	transport	biological process	TAS[9845349]	47

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 2)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
SLC6A5	STX1A	NO	in vitro	15276154
SLC6A5	SDCBP	NO	in vitro;in vivo;yeast 2-hybrid	15276154

Related other genetic factors

Gene related SNPs (count: 17)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs2000959	chr11:20637133 - 20637133(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
rs2241940	chr11:20600804 - 20600804(1)	intron_variant; NMD_transcript_variant	1(0/1/0)
rs1805091	chr11:20626834 - 20626834(1)	3_prime_UTR_variant; missense_variant; NMD_transcript_variant; upstream_gene_variant	1(0/1/0)
rs2289683	chr11:20614865 - 20614865(1)	intron_variant; NMD_transcript_variant	1(0/1/0)

rs_ID	Location	Functional Annotation
rs16906549	chr11:20614120 - 20614120(1)	intron_variant; NMD_transcript_variant
rs16906566	chr11:20617516 - 20617516(1)	intron_variant; NMD_transcript_variant
rs7925624	chr11:20617919 - 20617919(1)	intron_variant; NMD_transcript_variant
rs2298825	chr11:20638137 - 20638137(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1945773	chr11:20640344 - 20640344(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs10833371	chr11:20639560 - 20639560(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs1945774	chr11:20643858 - 20643858(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs17298460	chr11:20642894 - 20642894(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs883377	chr11:20622581 - 20622581(1)	intron_variant; NMD_transcript_variant
rs1894163	chr11:20623214 - 20623214(1)	intron_variant; NMD_transcript_variant
rs12803296	chr11:20624802 - 20624802(1)	intron_variant; NMD_transcript_variant; upstream_gene_variant
rs11025658	chr11:20623449 - 20623449(1)	intron_variant; NMD_transcript_variant
rs11025659	chr11:20624453 - 20624453(1)	intron_variant; NMD_transcript_variant; 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)
SLC6A5_AC-tandem-repeat	microsatellite		1 (0/1/0)

Gene related regions (count: 2)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 11	chr11:0-135086622	2 (0/2/0)
11p15	chr11:0-22000000	5 (0/4/1)

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

Gene relationship with SZ

Reference	Description	Result Category
16691125	Our results do not suggest that a common genetic variant at the GLYT2 locus contributes to BPAD and/or schizophrenia in patients of German descent.	Negative

Reference	ID in SZGene	Result Category
18638388	109	Positive
16691125	109	Negative

Gene relationship with MDD

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Region: chr11:20599400..20659285 View in gBrowse