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

Gene ID: 1497, updated on 5-Feb-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
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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

    UniProtKB/TrEMBL
    Q6FGP9
  2. XM_054315234.1XP_054171209.1  cystinosin isoform X1

    UniProtKB/TrEMBL
    Q6FGP9
  3. XM_054315236.1XP_054171211.1  cystinosin isoform X3

    UniProtKB/TrEMBL
    B4DJQ1

RNA

  1. XR_008484790.1 RNA Sequence