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

Gene ID: 1497, updated on 23-May-2015
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
See CTNS in MapViewer
Location:
17p13
Exon count:
12
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 17 NC_000017.11 (3636468..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/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 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 (human T-cell leukemia virus type I) 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...

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 
Process Evidence Code Pubs
ATP metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
L-cystine transport IDA
Inferred from Direct Assay
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 IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
cystinosin
Names
cystinosin

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
    Conserved Domains (2) summary
    TIGR00951
    Location:125357
    Cystine_transporter; 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
    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 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p2 Primary Assembly

    Range
    3636468..3663103
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005256485.1XP_005256542.1  

    See identical proteins and their annotated locations for XP_005256542.1

    UniProtKB/Swiss-Prot
    O60931
    Related
    ENSP00000046640, OTTHUMP00000197111, ENST00000046640, OTTHUMT00000317696
    Conserved Domains (2) summary
    TIGR00951
    Location:125357
    Cystine_transporter; Lysosomal Cystine Transporter
    pfam04193
    Location:126186
    PQ-loop; PQ loop repeat
  2. XM_006721464.1XP_006721527.1  

    See identical proteins and their annotated locations for XP_006721527.1

    Conserved Domains (2) summary
    TIGR00951
    Location:1210
    Cystine_transporter; Lysosomal Cystine Transporter
    pfam04193
    Location:118178
    PQ-loop; PQ loop repeat
  3. XM_011523692.1XP_011521994.1  

    See identical proteins and their annotated locations for XP_011521994.1

    Conserved Domains (2) summary
    TIGR00951
    Location:1210
    Cystine_transporter; Lysosomal Cystine Transporter
    pfam04193
    Location:118178
    PQ-loop; PQ loop repeat
  4. XM_006721463.1XP_006721526.1  

    See identical proteins and their annotated locations for XP_006721526.1

    UniProtKB/Swiss-Prot
    O60931
    Related
    ENSP00000371294, OTTHUMP00000115861, ENST00000381870, OTTHUMT00000207377
    Conserved Domains (2) summary
    TIGR00951
    Location:125357
    Cystine_transporter; Lysosomal Cystine Transporter
    pfam04193
    Location:126186
    PQ-loop; PQ loop repeat
  5. XM_011523691.1XP_011521993.1  

    See identical proteins and their annotated locations for XP_011521993.1

    Conserved Domains (2) summary
    TIGR00951
    Location:125357
    Cystine_transporter; Lysosomal Cystine Transporter
    pfam04193
    Location:126186
    PQ-loop; PQ loop repeat

RNA

  1. XR_934003.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018928.2 Alternate CHM1_1.1

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