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    CTNS cystinosin, lysosomal cystine transporter [ Homo sapiens (human) ]

    Gene ID: 1497, updated on 8-Aug-2016
    Official Symbol
    CTNSprovided by HGNC
    Official Full Name
    cystinosin, lysosomal cystine transporterprovided by HGNC
    Primary source
    HGNC:HGNC:2518
    See related
    Ensembl:ENSG00000040531 HPRD:05885; MIM:606272; Vega:OTTHUMG00000090693
    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
    PQLC4; CTNS-LSB
    Summary
    This gene encodes a seven-transmembrane domain protein that functions to transport cystine out of lysosomes. Its activity is driven by the H+ electrochemical gradient of the lysosomal membrane. Mutations in this gene cause cystinosis, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]
    Orthologs
    Location:
    17p13
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 17 NC_000017.11 (3636391..3663103)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (3539762..3566397)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene transient receptor potential cation channel subfamily V member 1 Neighboring gene pterin-4 alpha-carbinolamine dehydratase 2 pseudogene Neighboring gene sedoheptulokinase Neighboring gene uncharacterized LOC105371493 Neighboring gene uncharacterized LOC105371492 Neighboring gene P2RX5-TAX1BP3 readthrough (NMD candidate) Neighboring gene ribosomal protein L21 pseudogene 125 Neighboring gene Tax1 binding protein 3 Neighboring gene ER membrane protein complex subunit 6

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • Lysosome, organism-specific biosystem (from KEGG)
      Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
    • Lysosome, conserved biosystem (from KEGG)
      Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
    • Miscellaneous transport and binding events, organism-specific biosystem (from REACTOME)
      Miscellaneous transport and binding events, organism-specific biosystemThis section contains known transport and binding events that as of yet cannot be placed in exisiting pathways (Purves 2001, He et al. 2009, Rees et al. 2009).
    • SLC-mediated transmembrane transport, organism-specific biosystem (from REACTOME)
      SLC-mediated transmembrane transport, organism-specific biosystemProteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the m...
    • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
      Transmembrane transport of small molecules, organism-specific biosystem
      Transmembrane transport of small molecules
    • Transport of inorganic cations/anions and amino acids/oligopeptides, organism-specific biosystem (from REACTOME)
      Transport of inorganic cations/anions and amino acids/oligopeptides, organism-specific biosystemTeleologically, one might argue that inorganic cation and anion transport would be evolutionarily among the oldest transport functions. Eight families comprise the group that transports exclusively i...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    L-cystine transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    L-cystine transmembrane transporter activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    L-cystine transmembrane transporter activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    ATP metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    L-cystine transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    L-cystine transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
     
    brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular amino acid metabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cognition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    glutathione metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    grooming behavior IEA
    Inferred from Electronic Annotation
    more info
     
    ion transport TAS
    Traceable Author Statement
    more info
     
    lens development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    long-term memory IEA
    Inferred from Electronic Annotation
    more info
     
    melanin biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    transmembrane transport TAS
    Traceable Author Statement
    more info
     
    visual learning IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    NOT early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    intermediate filament cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    melanosome IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    cystinosin
    Names
    cystinosis nephropathic

    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_012489.1 RefSeqGene

      Range
      5001..31636
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001031681.2NP_001026851.2  cystinosin isoform 1 precursor

      See identical proteins and their annotated locations for NP_001026851.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript but encodes the longer isoform (1).
      Source sequence(s)
      AC027796, AC132942, BC032850, BX369529, CA454595, DB026195
      Consensus CDS
      CCDS32530.1
      UniProtKB/Swiss-Prot
      O60931
      UniProtKB/TrEMBL
      A0A0S2Z3I9
      Related
      ENSP00000371294, OTTHUMP00000115861, ENST00000381870, OTTHUMT00000207377
      Conserved Domains (2) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:126186
      PQ-loop; PQ loop repeat
    2. NM_004937.2NP_004928.2  cystinosin isoform 2 precursor

      See identical proteins and their annotated locations for NP_004928.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR and 3' coding region, compared to variant 1, resulting in an isoform (2) with a distinct and shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AC027796, AC132942, BC032850, BX369529, DB026195
      Consensus CDS
      CCDS11031.1
      UniProtKB/Swiss-Prot
      O60931
      UniProtKB/TrEMBL
      A0A0S2Z3K3
      Related
      ENSP00000046640, OTTHUMP00000197111, ENST00000046640, OTTHUMT00000317696
      Conserved Domains (2) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:126186
      PQ-loop; PQ loop repeat

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p7 Primary Assembly

      Range
      3636391..3663103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006721463.2XP_006721526.1  

      See identical proteins and their annotated locations for XP_006721526.1

      UniProtKB/TrEMBL
      A0A0S2Z3I9
      Conserved Domains (2) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:126186
      PQ-loop; PQ loop repeat
    2. XM_005256485.2XP_005256542.1  

      See identical proteins and their annotated locations for XP_005256542.1

      UniProtKB/TrEMBL
      A0A0S2Z3I9
      Conserved Domains (2) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:126186
      PQ-loop; PQ loop repeat
    3. XM_017024255.1XP_016879744.1  

    4. XM_006721464.2XP_006721527.1  

      See identical proteins and their annotated locations for XP_006721527.1

      Conserved Domains (2) summary
      TIGR00951
      Location:1210
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:118178
      PQ-loop; PQ loop repeat
    5. XM_017024257.1XP_016879746.1  

    6. XM_017024254.1XP_016879743.1  

    7. XM_017024256.1XP_016879745.1  

    8. XM_011523692.2XP_011521994.1  

      See identical proteins and their annotated locations for XP_011521994.1

      Conserved Domains (2) summary
      TIGR00951
      Location:1210
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:118178
      PQ-loop; PQ loop repeat
    9. XM_017024258.1XP_016879747.1  

    10. XM_011523691.2XP_011521993.1  

      See identical proteins and their annotated locations for XP_011521993.1

      UniProtKB/TrEMBL
      A0A0S2Z3I9
      Conserved Domains (2) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:126186
      PQ-loop; PQ loop repeat

    Alternate CHM1_1.1

    Genomic

    1. NC_018928.2 Alternate CHM1_1.1

      Range
      3550519..3577033
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)