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

Gene ID: 1497, updated on 24-Nov-2020

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
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

Genomic context

See CTNS in Genome Data Viewer
Location:
17p13.2
Exon count:
14
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (3636459..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

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-cystine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
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
 
negative regulation of hydrogen peroxide biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of mitochondrial membrane potential 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 HDA 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 HDA PubMed 
lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
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
 
vacuolar membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
cystinosin
Names
cystinosis nephropathic

NCBI Reference Sequences (RefSeq)

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
    5001..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/Swiss-Prot
    O60931
    UniProtKB/TrEMBL
    A0A0S2Z3I9
    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
    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
    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
    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
    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
    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
    O60931
    UniProtKB/TrEMBL
    A0A0S2Z3K3
    Related
    ENSP00000046640.3, ENST00000046640.8
    Conserved Domains (2) summary
    TIGR00951
    Location:125357
    2A43; Lysosomal Cystine Transporter
    pfam04193
    Location:128185
    PQ-loop; PQ loop repeat

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_006721464.2XP_006721527.1  cystinosin isoform X2

    See identical proteins and their annotated locations for XP_006721527.1

    Conserved Domains (2) summary
    TIGR00951
    Location:1210
    2A43; Lysosomal Cystine Transporter
    pfam04193
    Location:122175
    PQ-loop; PQ loop repeat
  2. XM_017024254.1XP_016879743.1  cystinosin isoform X2

    Related
    ENSP00000461118.2, ENST00000574776.6
    Conserved Domains (2) summary
    TIGR00951
    Location:1210
    2A43; Lysosomal Cystine Transporter
    pfam04193
    Location:122175
    PQ-loop; PQ loop repeat
  3. XM_011523692.2XP_011521994.1  cystinosin isoform X2

    See identical proteins and their annotated locations for XP_011521994.1

    Conserved Domains (2) summary
    TIGR00951
    Location:1210
    2A43; Lysosomal Cystine Transporter
    pfam04193
    Location:122175
    PQ-loop; PQ loop repeat
  4. XM_006721463.3XP_006721526.1  cystinosin isoform X1

    See identical proteins and their annotated locations for XP_006721526.1

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

    See identical proteins and their annotated locations for XP_011521993.1

    UniProtKB/TrEMBL
    A0A0S2Z3I9
    Conserved Domains (1) summary
    TIGR00951
    Location:125357
    2A43; Lysosomal Cystine Transporter
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