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

    Gene ID: 1497, updated on 3-Apr-2024

    Summary

    Official Symbol
    CTNSprovided by HGNC
    Official Full Name
    cystinosin, lysosomal cystine transporterprovided by HGNC
    Primary source
    HGNC:HGNC:2518
    See related
    Ensembl:ENSG00000040531 MIM:606272; AllianceGenome:HGNC:2518
    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; SLC66A4; 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]
    Expression
    Ubiquitous expression in testis (RPKM 9.6), adrenal (RPKM 5.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CTNS in Genome Data Viewer
    Location:
    17p13.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (3636459..3663103)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (3525479..3552155)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (3539753..3566397)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:3478292-3479491 Neighboring gene transient receptor potential cation channel subfamily V member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3497604-3498104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3512595-3513096 Neighboring gene pterin-4 alpha-carbinolamine dehydratase 2 pseudogene Neighboring gene sedoheptulokinase Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:3526895-3528094 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:3537096-3537961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8015 Neighboring gene uncharacterized LOC105371493 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:3543723-3544266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3557631-3558349 Neighboring gene P2RX5-TAX1BP3 readthrough (NMD candidate) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3570666-3571197 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:3571198-3571728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8017 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3572261-3572791 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3572792-3573322 Neighboring gene ribosomal protein L21 pseudogene 125 Neighboring gene Tax1 binding protein 3 Neighboring gene ER membrane protein complex subunit 6

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in ATP metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in L-cystine transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in L-cystine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in L-cystine transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in L-cystine transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in amino acid metabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in brush border assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cognition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glutathione metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in grooming behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lens development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in long-term memory IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in melanin biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in monoatomic ion transport TAS
    Traceable Author Statement
    more info
     
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of hydrogen peroxide biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of TORC1 signaling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of mitochondrial membrane potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of thyroid hormone generation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proton transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proximal tubule morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of TORC1 signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of melanin biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in renal albumin absorption IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in renal glucose absorption IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in renal phosphate ion absorption IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in renal water absorption IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in thyroid gland development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transmembrane transport TAS
    Traceable Author Statement
    more info
     
    involved_in visual learning IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    NOT located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane HDA PubMed 
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in melanosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in melanosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    cystinosin
    Names
    cystinosis nephropathic

    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_012489.2 RefSeqGene

      Range
      5293..31636
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001031681.3NP_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/TrEMBL
      A0A0S2Z3I9, Q6FGP9
      Related
      ENSP00000371294.3, ENST00000381870.8
      Conserved Domains (1) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
    2. NM_001374492.1NP_001361421.1  cystinosin isoform 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AC027796, AC132942, AK292019
      Consensus CDS
      CCDS32530.1
      UniProtKB/TrEMBL
      A0A0S2Z3I9, Q6FGP9
      Conserved Domains (1) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
    3. NM_001374493.1NP_001361422.1  cystinosin isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC027796, AC132942
      Consensus CDS
      CCDS92228.1
      UniProtKB/TrEMBL
      A0A669KB82, B4DML6
      Conserved Domains (1) summary
      TIGR00951
      Location:1210
      2A43; Lysosomal Cystine Transporter
    4. NM_001374494.1NP_001361423.1  cystinosin isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC027796, AC132942
      Consensus CDS
      CCDS92228.1
      UniProtKB/TrEMBL
      A0A669KB82, B4DML6
      Conserved Domains (1) summary
      TIGR00951
      Location:1210
      2A43; Lysosomal Cystine Transporter
    5. NM_001374495.1NP_001361424.1  cystinosin isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC027796, AC132942
      Consensus CDS
      CCDS92228.1
      UniProtKB/TrEMBL
      A0A669KB82, B4DML6
      Conserved Domains (1) summary
      TIGR00951
      Location:1210
      2A43; Lysosomal Cystine Transporter
    6. NM_001374496.1NP_001361425.1  cystinosin isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC027796, AC132942
      Consensus CDS
      CCDS92228.1
      UniProtKB/TrEMBL
      A0A669KB82, B4DML6
      Related
      ENSP00000501123.1, ENST00000673669.1
      Conserved Domains (1) summary
      TIGR00951
      Location:1210
      2A43; Lysosomal Cystine Transporter
    7. NM_004937.3NP_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
      D3DTJ5, O60931, Q8IZ01, Q9UNK6
      UniProtKB/TrEMBL
      A0A0S2Z3K3, Q6FGP9
      Related
      ENSP00000046640.4, ENST00000046640.9
      Conserved Domains (2) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:128185
      PQ-loop; PQ loop repeat

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      3636459..3663103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006721463.4XP_006721526.1  cystinosin isoform X1

      See identical proteins and their annotated locations for XP_006721526.1

      UniProtKB/TrEMBL
      A0A0S2Z3I9, Q6FGP9
      Conserved Domains (1) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
    2. XM_011523691.3XP_011521993.1  cystinosin isoform X1

      See identical proteins and their annotated locations for XP_011521993.1

      UniProtKB/TrEMBL
      A0A0S2Z3I9, Q6FGP9
      Conserved Domains (1) summary
      TIGR00951
      Location:125357
      2A43; Lysosomal Cystine Transporter
    3. XM_011523692.3XP_011521994.1  cystinosin isoform X3

      See identical proteins and their annotated locations for XP_011521994.1

      UniProtKB/TrEMBL
      B4DJQ1, I3L4A9
      Related
      ENSP00000461118.2, ENST00000574776.6
      Conserved Domains (2) summary
      TIGR00951
      Location:1210
      2A43; Lysosomal Cystine Transporter
      pfam04193
      Location:122175
      PQ-loop; PQ loop repeat
    4. XM_047435501.1XP_047291457.1  cystinosin isoform X2

    RNA

    1. XR_007065277.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      3525479..3552155
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315235.1XP_054171210.1  cystinosin isoform X1

    2. XM_054315234.1XP_054171209.1  cystinosin isoform X1

    3. XM_054315236.1XP_054171211.1  cystinosin isoform X3

    RNA

    1. XR_008484790.1 RNA Sequence