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SLC6A9 Gene

protein-coding   GIFtS: 63
GCID: GC01M044462

Solute Carrier Family 6 (Neurotransmitter Transporter, Glycine),...

  See SLC6A9-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Solute Carrier Family 6 (Neurotransmitter Transporter, Glycine), Member
91 2
     Sodium- And Chloride-Dependent Glycine Transporter 12
Solute Carrier Family 6 Member 92 3     GlyT-13
GLYT12 5     GlyT13
glyT-12     

External Ids:    HGNC: 110561   Entrez Gene: 65362   Ensembl: ENSG000001965177   OMIM: 6010195   UniProtKB: P480673   
ORGUL members:         

Export aliases for SLC6A9 gene to outside databases

Previous GC identifers: GC01M044301 GC01M043463 GC01M043891 GC01M043876 GC01M044132 GC01M042577


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SLC6A9 Gene:
SLC6A9 (solute carrier family 6 (neurotransmitter transporter, glycine), member 9) is a protein-coding gene. Diseases associated with SLC6A9 include schizophrenia. GO annotations related to this gene include neurotransmitter:sodium symporter activity and glycine:sodium symporter activity. An important paralog of this gene is SLC6A6.

UniProtKB/Swiss-Prot: SC6A9_HUMAN, P48067
Function: Terminates the action of glycine by its high affinity sodium-dependent reuptake into presynaptic
terminals. May play a role in regulation of glycine levels in NMDA receptor-mediated neurotransmission

summary for SLC6A9 Gene:
Glycine transporters (GlyTs) belong to a family of high affinity Na+- and Cl--dependent neurotransmitter
transporters proteins. There are two subtypes of glycine transporters; GlyT1 and GlyT2. GlyT1s are
predominantly located on glia within caudal brain areas, the diencephalon and olfactory bulb. They regulate
synaptic glycine concentration, influencing NMDA receptor-mediated neurotransmission and are important in
neonatal life for regulating glycine concentrations at inhibitory glycinergic synapses. GlyT2s are
predominantly located on neurons within caudal brain areas, the spinal cord, brainstem and cerebellum. They
are crucial for efficient transmitter loading of synaptic vesicles and lack-of-function mutations are fatal
in the early neonatal period. Both GlyT1 and GlyT2 are unevenly distributed across the cell surface, which
is thought to optimize the removal of glycine from the extracellular compartment. Transport of glycine
involves co-transport of Na+ and Cl- ions. The Na+ concentration gradient is maintained by the plasma
membrane Na+,K+-ATPase and allows the accumulation of glycine against its concentration gradient. GlyTs are
glycosylated and this is necessary for the protein trafficking to the plasma membrane. Further regulatory
mechanisms of GlyTs include the presence of PKC, PKA and CaMK consensus sites, pH and syntaxin1 levels.
Pharmacologically, glycine transporter inhibitors may have applications in the treatment of muscle tone
defects, epilepsy, schizophrenia, pain and neurodegenerative disorders.

Gene Wiki entry for SLC6A9 (Glycine transporter 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC6A9 gene promoter:
         MZF-1   NCX/Ncx   Lmo2   CUTL1   Zic3   MRF-2   GATA-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SLC6A9 promoter sequence
   Search Chromatin IP Primers for SLC6A9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC6A9


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p33   Ensembl cytogenetic band:  1p34.1   HGNC cytogenetic band: 1p33

SLC6A9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC6A9 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M044462:  view genomic region     (about GC identifiers)

Start:
44,457,172 bp from pter      End:
44,497,139 bp from pter
Size:
39,968 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SC6A9_HUMAN, P48067 (See protein sequence)
Recommended Name: Sodium- and chloride-dependent glycine transporter 1  
Size: 706 amino acids; 78260 Da
Sequence caution: Sequence=AAB30784.1; Type=Frameshift; Positions=8; Sequence=AAB30785.1; Type=Frameshift;
Positions=8; Sequence=CAI19428.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=CAI19429.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: A6NDH1 A6NII2 A6NNZ8 Q5TAB8 Q5TAB9 Q5TAC0
Alternative splicing: 3 isoforms:  P48067-1   P48067-2   P48067-3   

Explore the universe of human proteins at neXtProt for SLC6A9: NX_P48067

Explore proteomics data for SLC6A9 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn250, Asn256
  • Modification sites at PhosphoSitePlus

  • See SLC6A9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001020016.1  NP_001248309.1  NP_008865.2  NP_964012.2  

    ENSEMBL proteins: 
     ENSP00000361381   ENSP00000361380   ENSP00000361384   ENSP00000434460   ENSP00000353791  
     ENSP00000350362   ENSP00000435652   ENSP00000433241   ENSP00000442523  
    Reactome Protein details: P48067

    SLC6A9 Human Recombinant Protein Products:

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    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for SLC6A9 

     
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    antibodies-online peptides for SLC6A9

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    antibodies-online antibodies for SLC6A9 (23 products) 

    SLC6A9 Assay Products:

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    antibodies-online kits for SLC6A9 (10 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SLC: Solute carriers

    IUPHAR Guide to PHARMACOLOGY protein family classification: GlyT1
    Glycine transporter subfamily

    2 InterPro protein domains:
     IPR000175 Na/ntran_symport
     IPR003028 Na/ntran_symport_glycine_GLY1

    Graphical View of Domain Structure for InterPro Entry P48067

    ProtoNet protein and cluster: P48067

    1 Blocks protein domain: IPB003028 Glycine neurotransmitter transporter type 1 (GLYT-1) signature

    UniProtKB/Swiss-Prot: SC6A9_HUMAN, P48067
    Similarity: Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A9 subfamily


    Find genes that share domains with SLC6A9           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SC6A9_HUMAN, P48067
    Function: Terminates the action of glycine by its high affinity sodium-dependent reuptake into presynaptic
    terminals. May play a role in regulation of glycine levels in NMDA receptor-mediated neurotransmission

         Genatlas biochemistry entry for SLC6A9:
    solute carrier family 6,member A9,neurotransmitter transporter,glycine

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005283sodium:amino acid symporter activity ----
    GO:0005328neurotransmitter:sodium symporter activity IEA--
    GO:0005515protein binding ----
    GO:0015187glycine transmembrane transporter activity ----
    GO:0015375glycine:sodium symporter activity TAS8183239
         
    Find genes that share ontologies with SLC6A9           About GenesLikeMe


    Phenotypes:
         10 MGI mutant phenotypes (inferred from 7 alleles(MGI details for Slc6a9):
     behavior/neurological  growth/size/body  homeostasis/metabolism  integument  mortality/aging 
     muscle  nervous system  no phenotypic analysis  normal  respiratory system 

    Find genes that share phenotypes with SLC6A9           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for SLC6A9: Slc6a9tm1Jtc Slc6a9tm1.1Blt Slc6a9tm1Betz

       genOway: Develop your customized and physiologically relevant rodent model for SLC6A9

    miRNA
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    miRTarBase miRNAs that target SLC6A9:
    hsa-mir-7-5p (MIRT025716), hsa-mir-335-5p (MIRT017329), hsa-mir-103a-3p (MIRT027081), hsa-mir-26b-5p (MIRT029053), hsa-mir-221-3p (MIRT024167)

    Block miRNA regulation of human, mouse, rat SLC6A9 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SLC6A9 (see all 44):
    hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-106a hsa-miR-200a hsa-miR-30d hsa-miR-141 hsa-miR-372
    SwitchGear 3'UTR luciferase reporter plasmidSLC6A9 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC6A9


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SC6A9_HUMAN, P48067: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    golgi apparatus1
    nucleus1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane IEA--
    GO:0016020membrane TAS8183239
    GO:0016021integral component of membrane ----

    Find genes that share ontologies with SLC6A9           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SLC6A9 About    
    See pathways by source

    SuperPathContained pathways About
    1Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
    SLC-mediated transmembrane transport0.47
    Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds0.38
    Transmembrane transport of small molecules0.47
    Na+/Cl- dependent neurotransmitter transporters0.00


    Find genes that share SuperPaths with SLC6A9           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for SLC6A9
        Na+/Cl- dependent neurotransmitter transporters


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SLC6A9
    Interactions:

        Search GeneGlobe Interaction Network for SLC6A9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 15)

    Selected Interacting proteins for SLC6A9 (P480673 ENSP000003613814) via UniProtKB, MINT, STRING, and/or I2D (see all 16)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GABRR1P240463, ENSP000004126734I2D: score=1 STRING: ENSP00000412673
    ITGA1P561993, ENSP000002825884I2D: score=1 STRING: ENSP00000282588
    PRKCAP172523, ENSP000002843844I2D: score=2 STRING: ENSP00000284384
    STX1AQ166233, ENSP000002228124I2D: score=4 STRING: ENSP00000222812
    DLG4P783523I2D: score=1 
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport TAS8183239
    GO:0006836neurotransmitter transport ----
    GO:0015816glycine transport ----
    GO:0055085transmembrane transport TAS--

    Find genes that share ontologies with SLC6A9           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Compounds for SLC6A9 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    Org 25543 hydrochloridePotent and selective GlyT2 inhibitor[495076-64-7]
    LY 2365109 hydrochloridePotent and selective GlyT1 inhibitor[868265-28-5]
    ALX 5407 hydrochlorideSelective non-transportable GlyT1 inhibitor[571147-18-7]
    NFPSSelective non-transportable GlyT1 inhibitor[405225-21-0]
    Org 24598 lithium saltSelective GlyT1 inhibitor[722456-08-8]

    2 HMDB Compounds for SLC6A9    About this table
    CompoundSynonyms CAS #PubMed Ids
    Glycine2-Aminoacetate (see all 15)56-40-6--
    SodiumSodium (see all 2)7440-23-5--

    1 DrugBank Compound for SLC6A9    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Glycine2-Aminoacetic acid (see all 4)56-40-6target--17597258 17017963 16899062 17504107 17462677

    Selected IUPHAR Ligands for SLC6A9 (GlyT1) (see all 17)    About this table
    LigandTypeActionAffinityPubmed IDs
    (R)-NFPS
    InhibitorInhibition8.5 - 9.1--
    [3H](R)-NPTS
    NoneNone9--
    [3H]GSK931145
    NoneNone8.8--
    [3H]SB-733993
    NoneNone8.7--
    SSR-103800
    InhibitorInhibition8.7--
    [35S]ACPPB
    NoneNone8.7--
    N-methyl-SSR504734
    InhibitorInhibition8.6--
    [3H]N-methyl-SSR504734
    NoneNone8.1 - 8.5--
    NFPS
    InhibitorInhibition7 - 8.5--
    [3H]NFPS
    NoneNone7.7 - 8.2--

    4 Novoseek inferred chemical compound relationships for SLC6A9 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sarcosine 91.3 9 17017963 (2), 16143353 (2), 14622582 (1), 16611082 (1) (see all 5)
    nmda 70.1 37 17017963 (2), 16611082 (2), 17504107 (2), 14622582 (1) (see all 19)
    strychnine 69.6 2 17522628 (2)
    glutamate 44.1 2 10366190 (1)



    Find genes that share compounds with SLC6A9           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SLC6A9 gene (4 alternative transcripts): 
    NM_001024845.2  NM_001261380.1  NM_006934.3  NM_201649.3  

    Unigene Cluster for SLC6A9:

    Solute carrier family 6 (neurotransmitter transporter, glycine), member 9
    Hs.442590  [show with all ESTs]
    Unigene Representative Sequence: NM_201649
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372307(uc009vxe.2 uc010okm.1) ENST00000372306 ENST00000372310(uc001cll.3 uc001clm.3 uc009vxd.3 uc010okn.2 uc001cln.3 uc010oko.2)
    ENST00000475075 ENST00000360584 ENST00000357730 ENST00000492434 ENST00000528803
    ENST00000489764 ENST00000466926 ENST00000533007 ENST00000537678(uc010okp.1)

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    Additional mRNA sequence: 

    AK296438.1 AK298611.1 AK311136.1 AK315233.1 AK315933.1 CR749669.1 NR_048548.1 NR_048549.1 
    S70609.1 S70612.1 

    6 DOTS entries:

    DT.99989961  DT.92417826  DT.91709090  DT.92070708  DT.100746929  DT.437254 

    Selected AceView cDNA sequences (see all 40):

    BQ923735 BI255536 BU951393 BF992593 AU280413 BQ054651 BI038652 BU951656 
    BQ055381 BU072450 BI253460 BE546296 AI884725 S70609 CR749669 BE089941 
    NM_201649 NM_006934 CB053517 S70612 BP350680 BX283195 R16457 BQ643194 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SLC6A9 (see all 7)    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16
    SP1:                          -                 -                                                                     
    SP2:                          -     -           -                                                                     
    SP3:              -     -     -     -           -                                                                     
    SP4:              -     -     -     -     -     -     -                                                               
    SP5:              -     -     -                                                                                       


    ECgene alternative splicing isoforms for SLC6A9

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SLC6A9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCCTCCCCT
    SLC6A9 Expression
    About this image


    SLC6A9 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Neurons
             AII Amacrine Cells Inner Nuclear Layer
     
     Eye (Sensory Organs)    fully expand to see all 10 entries
             AII Amacrine Cells Inner Nuclear Layer
     
     Neural Tube (Nervous System)    fully expand to see all 4 entries
             Mesencephalic Ventricular Zone
     
     Liver (Hepatobiliary System)
             Liver Lobule
     
     Brain (Nervous System)
             Cerebellum
    SLC6A9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLC6A9 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.442590

    UniProtKB/Swiss-Prot: SC6A9_HUMAN, P48067
    Tissue specificity: Isoform GlyT-1A and isoform GlyT-1B can be found in brain, kidney, pancreas, lung, placenta
    and liver but isoform GlyT-1C is only found in brain

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SLC6A9 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slc6a91 , 5 solute carrier family 6 (neurotransmitter transporter, more1, 5 90.64(n)1
    96.95(a)1
      4 (53.62 cM)5
    146641  NM_008135.41  NP_032161.21 
     1178345065 
    chicken
    (Gallus gallus)
    Aves SLC6A91 solute carrier family 6 (neurotransmitter transporter, more 82.14(n)
    84.69(a)
      424576  NM_001031279.1  NP_001026450.1 
    lizard
    (Anolis carolinensis)
    Reptilia SLC6A96
    solute carrier family 6 (neurotransmitter transpor...
    83(a)
    1 ↔ 1
    4(108950799-109019948)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia slc6a91 solute carrier family 6 (neurotransmitter transporter, more 72.35(n)
    82.48(a)
      100492204  XM_004913970.1  XP_004914027.1 
    zebrafish
    (Danio rerio)
    Actinopterygii slc6a91 solute carrier family 6 (neurotransmitter transporter, more 72.9(n)
    78.54(a)
      494490  NM_001030073.1  NP_001025244.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG55493
    Ntl1
    glycine:sodium symporter3
    Neurotransmitter transporter-like1
    48(a)
    (best of 8)3
    53.42(n)1
    43.85(a)1
      340461  NM_135291.21  NP_609135.11 


    ENSEMBL Gene Tree for SLC6A9 (if available)
    TreeFam Gene Tree for SLC6A9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SLC6A9 gene
    SLC6A62  SLC6A112  SLC6A122  SLC6A82  SLC6A52  SLC6A142  SLC6A12  SLC6A32  
    SLC6A42  SLC6A132  SLC6A22  SLC6A72  
    Selected SIMAP similar genes for SLC6A9 using alignment to 7 protein entries:     SC6A9_HUMAN (see all proteins) (see all similar genes):
    SLC6A4    DAT1    SLC6A13    SLC6A7    SLC6A5    SLC6A3
    5HTT    SLC6A1    SLC6A6    SLC6A11    SLC6A12    SLC6A8
    SLC6A15    SLC6A2    SLC6A14    SLC6A16    SLC6A18    SLC6A19

    Find genes that share paralogs with SLC6A9           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for SLC6A9
    PGOHUM00000258019


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SLC6A9 (see all 1012)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1939210021,2
    Cuntested144474038(-) CCAGCA/GAGGAG 10 K E mis10--------
    rs1156954791,2
    C--44462774(+) TCCCCC/TAGCCC 6 -- ut31 nc-transcript-variant1Minor allele frequency- T:0.01NA 120
    rs1415766211,2
    C--44462854(+) AGCACG/TAGTCA 6 -- ut31 nc-transcript-variant0--------
    rs1915727891,2
    --44462880(+) ACCCAC/GAACCT 6 -- ut31 nc-transcript-variant0--------
    rs351813361,2
    C,F,H--44462912(+) GGTATC/TGGAGG 6 -- ut31 nc-transcript-variant4Minor allele frequency- T:0.01NS NA 232
    rs1829057401,2
    C--44462979(+) TTGGAC/TCTCCC 6 -- ut31 nc-transcript-variant0--------
    rs797764711,2
    C--44462997(+) CTCCAC/TTCCCA 6 -- ut31 nc-transcript-variant1Minor allele frequency- T:0.01NA 120
    rs1393787171,2
    C--44463169(+) CTCTGC/TGGTGG 6 -- ut31 nc-transcript-variant0--------
    rs22482531,2
    C,F,A,H--44463170(+) TCTGCG/AGTGGG 6 -- ut31 nc-transcript-variantese311Minor allele frequency- A:0.15NS EA NA WA EU 1218
    rs2015498641,2
    C--44463178(+) GGGAGC/GACGGG 6 -- ut31 nc-transcript-variant0--------

    HapMap Linkage Disequilibrium report for SLC6A9 (44457172 - 44497139 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SLC6A9:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv519538CNV Loss19592680
    nsv870606CNV Loss21882294
    nsv829704CNV Loss17160897

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601019    OMIM disorders: --

    1 disease for SLC6A9:    
    About MalaCards
    schizophrenia


    Find genes that share disorders with SLC6A9           About GenesLikeMe

    3 Novoseek inferred disease relationships for SLC6A9 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hypofunction 75.4 8 9861038 (1), 18355687 (1), 16841561 (1), 16719816 (1) (see all 6)
    schizophrenia 61.4 39 16604304 (4), 16841561 (3), 18638388 (3), 20166956 (1) (see all 14)
    psychotic 24.3 2 16604304 (1), 19051137 (1)

    Genetic Association Database (GAD): SLC6A9
    Human Genome Epidemiology (HuGE) Navigator: SLC6A9 (7 documents)

    Export disorders for SLC6A9 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SLC6A9 gene, integrated from 10 sources (see all 84):
    (articles sorted by number of sources associating them with SLC6A9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning of the human glycine transporter type 1: molecular and pharmacological characterization of novel isoform variants and chromosomal localization of the gene in the human and mouse genomes. (PubMed id 8183239)1, 2, 3 Kim K.-M.... Giros B. (Mol. Pharmacol. 1994)
    2. The glycine transporter 1 gene (GLYT1) is associated with methamphetamine-use disorder. (PubMed id 17582620)1, 4, 9 Morita Y....Kuroda S. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2008)
    3. Association study of polymorphisms in glycine transporter with schizophrenia. (PubMed id 16604304)1, 4, 9 Tsai S.J....Liou Y.J. (J Neural Transm 2006)
    4. Polymorphisms in glycine transporter with schizophrenia. (PubMed id 16841561)1, 4, 9 Tsai S.J....Liou Y.J. (Neuropsychopharmacol Hung 2006)
    5. Association study of polymorphisms in the neutral amino acid transporter genes SLC1A4, SLC1A5 and the glycine transporter genes SLC6A5, SLC6A9 with schizophrenia. (PubMed id 18638388)1, 4, 9 Deng X....Fukumaki Y. (BMC Psychiatry 2008)
    6. Association of SLC6A9 gene variants with human essential hypertension. (PubMed id 19556729)1, 4 Ueno T....Soma M. (J. Atheroscler. Thromb. 2009)
    7. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PubMed id 19086053)1, 4 GratacA^s M....Carracedo A. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2009)
    8. No association of alcohol dependence with SLC6A5 and SLC6A9 glycine transporter polymorphisms. (PubMed id 19650813)1, 4 Koller G....Preuss U.W. (Addict Biol 2009)
    9. Assignment of SLC6A9 to human chromosome band 1p33 by in situ hybridization. (PubMed id 7587377)1, 3 Jones E.M....Le Beau M.M. (Cytogenet. Cell Genet. 1995)
    10. Progress in the preparation and testing of glycine transporter type-1 (GlyT1) inhibitors. (PubMed id 17017963)7, 9 Lindsley C.W....Kinney G.G. (Curr Top Med Chem 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6536 HGNC: 11056 AceView: SLC6A9 Ensembl:ENSG00000196517 euGenes: HUgn6536
    ECgene: SLC6A9 H-InvDB: SLC6A9

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for SLC6A9 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SLC6A9 gene:
    Search GeneIP for patents involving SLC6A9

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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