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    SLC6A9 solute carrier family 6 member 9 [ Homo sapiens (human) ]

    Gene ID: 6536, updated on 1-Mar-2024

    Summary

    Official Symbol
    SLC6A9provided by HGNC
    Official Full Name
    solute carrier family 6 member 9provided by HGNC
    Primary source
    HGNC:HGNC:11056
    See related
    Ensembl:ENSG00000196517 MIM:601019; AllianceGenome:HGNC:11056
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GLYT1; GCENSG
    Summary
    The amino acid glycine acts as an inhibitory neurotransmitter in the central nervous system. The protein encoded by this gene is one of two transporters that stop glycine signaling by removing it from the synaptic cleft. [provided by RefSeq, Jun 2016]
    Expression
    Broad expression in skin (RPKM 13.4), adrenal (RPKM 9.7) and 18 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC6A9 in Genome Data Viewer
    Location:
    1p34.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (43996483..44031462, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (43859929..43902553, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (44462155..44497134, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44440619-44441451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44443584-44444175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44444176-44444766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44444767-44445358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44447723-44448312 Neighboring gene ATPase H+ transporting V0 subunit b Neighboring gene beta-1,4-galactosyltransferase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 801 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 802 Neighboring gene Sharpr-MPRA regulatory region 11322 Neighboring gene coiled-coil domain containing 24 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:44471356-44471562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44476286-44476951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44494509-44495068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44495069-44495626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 804 Neighboring gene uncharacterized LOC107984948 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44496268-44496864 Neighboring gene uncharacterized LOC124904168 Neighboring gene VISTA enhancer hs1857 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:44507734-44507907 Neighboring gene uncharacterized LOC124904169 Neighboring gene KLF transcription factor 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 806

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Atypical glycine encephalopathy
    MedGen: C4310943 OMIM: 617301 GeneReviews: GLYT1 Encephalopathy
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp547A1118

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables glycine transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables glycine transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables glycine:sodium symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables glycine:sodium symporter activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    involved_in glycine import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in glycine import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glycine import across plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in glycine transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of negative regulation of NMDA glutamate receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neurotransmitter transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of heme biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of hemoglobin biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of synaptic transmission, glycinergic ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in synaptic transmission, glycinergic IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in basal plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in dense core granule ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in hippocampal mossy fiber to CA3 synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in parallel fiber to Purkinje cell synapse IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in presynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    sodium- and chloride-dependent glycine transporter 1
    Names
    glyT-1
    solute carrier family 6 (neurotransmitter transporter, glycine), member 9

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_050929.1 RefSeqGene

      Range
      5031..40010
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001024845.3NP_001020016.1  sodium- and chloride-dependent glycine transporter 1 isoform 3

      See identical proteins and their annotated locations for NP_001020016.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding region compared to variant 2. The resulting isoform (3) is shorter and has a distinct N-terminus compared to isoform 2. Variants 3 and 9 both encode the same isoform (3).
      Source sequence(s)
      AI884725, AL139220, CN354684, S70609
      Consensus CDS
      CCDS30695.1
      UniProtKB/Swiss-Prot
      P48067
      Related
      ENSP00000361384.4, ENST00000372310.8
      Conserved Domains (1) summary
      cd11498
      Location:11594
      SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
    2. NM_001261380.2NP_001248309.1  sodium- and chloride-dependent glycine transporter 1 isoform 4

      See identical proteins and their annotated locations for NP_001248309.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region compared to variant 2. The resulting protein (isoform 4) is shorter compared to isoform 2.
      Source sequence(s)
      AK296438, AL139220, DA403430
      UniProtKB/TrEMBL
      B7Z3W8
      Conserved Domains (1) summary
      cd11498
      Location:30598
      SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
    3. NM_001328626.2NP_001315555.1  sodium- and chloride-dependent glycine transporter 1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (5) is shorter at the N-terminus compared to isoform 2.
      Source sequence(s)
      AL139220
      Consensus CDS
      CCDS85966.1
      UniProtKB/TrEMBL
      B7Z589
      Related
      ENSP00000434460.1, ENST00000475075.6
      Conserved Domains (1) summary
      cl00456
      Location:1483
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    4. NM_001328627.1NP_001315556.1  sodium- and chloride-dependent glycine transporter 1 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate exon in the 5' end compared to variant 2. The resulting isoform (6) has a shorter and distinct N-terminus compared to isoform 2.
      Source sequence(s)
      AL139220
      Conserved Domains (1) summary
      cl00456
      Location:42573
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    5. NM_001328628.1NP_001315557.1  sodium- and chloride-dependent glycine transporter 1 isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) lacks two alternate exons in the 5' end compared to variant 2. The resulting isoform (7) has a shorter and distinct N-terminus compared to isoform 2.
      Source sequence(s)
      AL139220
      Conserved Domains (1) summary
      cl00456
      Location:30529
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    6. NM_001328629.1NP_001315558.1  sodium- and chloride-dependent glycine transporter 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 2. Variants 3 and 9 both encode the same isoform (3).
      Source sequence(s)
      AL139220
      Consensus CDS
      CCDS30695.1
      UniProtKB/Swiss-Prot
      P48067
      Related
      ENSP00000501314.1, ENST00000673836.1
      Conserved Domains (1) summary
      cd11498
      Location:11594
      SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
    7. NM_001328630.2NP_001315559.1  sodium- and chloride-dependent glycine transporter 1 isoform 8

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) differs in the 5' UTR and coding sequence and lacks an alternate 3' in-frame exon compared to variant 2. The resulting isoform (8) is shorter at the N-terminus and lacks an alternate C-terminal segment compared to isoform 2.
      Source sequence(s)
      AL139220
    8. NM_006934.4NP_008865.2  sodium- and chloride-dependent glycine transporter 1 isoform 1

      See identical proteins and their annotated locations for NP_008865.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 2. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 2.
      Source sequence(s)
      AI884725, AL139220, S70612
      Consensus CDS
      CCDS41316.1
      UniProtKB/Swiss-Prot
      P48067
      Related
      ENSP00000350362.2, ENST00000357730.6
      Conserved Domains (1) summary
      cd11498
      Location:30613
      SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
    9. NM_201649.4NP_964012.2  sodium- and chloride-dependent glycine transporter 1 isoform 2

      See identical proteins and their annotated locations for NP_964012.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
      Source sequence(s)
      AI884725, AL139220, S70609
      Consensus CDS
      CCDS41317.1
      UniProtKB/Swiss-Prot
      A6NDH1, A6NII2, A6NNZ8, P48067, Q5TAB8, Q5TAB9, Q5TAC0
      Related
      ENSP00000353791.2, ENST00000360584.6
      Conserved Domains (1) summary
      cd11498
      Location:84667
      SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain

    RNA

    1. NR_048548.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate 5' exon compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK315233, AL139220

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      43996483..44031462 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428739.1XP_047284695.1  sodium- and chloride-dependent glycine transporter 1 isoform X1

    2. XM_047428740.1XP_047284696.1  sodium- and chloride-dependent glycine transporter 1 isoform X2

    3. XM_017002152.3XP_016857641.1  sodium- and chloride-dependent glycine transporter 1 isoform X4

    4. XM_047428744.1XP_047284700.1  sodium- and chloride-dependent glycine transporter 1 isoform X6

      UniProtKB/TrEMBL
      J3KPA5
      Related
      ENSP00000361380.3, ENST00000372306.7
    5. XM_047428743.1XP_047284699.1  sodium- and chloride-dependent glycine transporter 1 isoform X5

    6. XM_011542017.3XP_011540319.1  sodium- and chloride-dependent glycine transporter 1 isoform X3

      Conserved Domains (1) summary
      cl00456
      Location:84585
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      43859929..43902553 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338436.1XP_054194411.1  sodium- and chloride-dependent glycine transporter 1 isoform X10

    2. XM_054338437.1XP_054194412.1  sodium- and chloride-dependent glycine transporter 1 isoform X10

    3. XM_054338430.1XP_054194405.1  sodium- and chloride-dependent glycine transporter 1 isoform X8

    4. XM_054338443.1XP_054194418.1  sodium- and chloride-dependent glycine transporter 1 isoform X12

      UniProtKB/TrEMBL
      B7Z3A9
    5. XM_054338435.1XP_054194410.1  sodium- and chloride-dependent glycine transporter 1 isoform X10

    6. XM_054338431.1XP_054194406.1  sodium- and chloride-dependent glycine transporter 1 isoform X8

    7. XM_054338432.1XP_054194407.1  sodium- and chloride-dependent glycine transporter 1 isoform X8

    8. XM_054338440.1XP_054194415.1  sodium- and chloride-dependent glycine transporter 1 isoform X11

    9. XM_054338434.1XP_054194409.1  sodium- and chloride-dependent glycine transporter 1 isoform X9

    10. XM_054338429.1XP_054194404.1  sodium- and chloride-dependent glycine transporter 1 isoform X7

    11. XM_054338433.1XP_054194408.1  sodium- and chloride-dependent glycine transporter 1 isoform X1

    12. XM_054338438.1XP_054194413.1  sodium- and chloride-dependent glycine transporter 1 isoform X2

    13. XM_054338441.1XP_054194416.1  sodium- and chloride-dependent glycine transporter 1 isoform X4

    14. XM_054338444.1XP_054194419.1  sodium- and chloride-dependent glycine transporter 1 isoform X6

      UniProtKB/TrEMBL
      J3KPA5
    15. XM_054338442.1XP_054194417.1  sodium- and chloride-dependent glycine transporter 1 isoform X5

    16. XM_054338439.1XP_054194414.1  sodium- and chloride-dependent glycine transporter 1 isoform X3