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

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: mouse all
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Genomic context

Location:: 17p13.2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (3636459..3663103)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (3525479..3552155)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (3539753..3566397)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Omic Studies on In Vitro Cystinosis Model: siRNA-Mediated CTNS Gene Silencing in HK-2 Cells.
Title: Omic Studies on In Vitro Cystinosis Model: siRNA-Mediated CTNS Gene Silencing in HK-2 Cells.
Studies with Human-Induced Pluripotent Stem Cells Reveal That CTNS Mutations Can Alter Renal Proximal Tubule Differentiation.
Title: Studies with Human-Induced Pluripotent Stem Cells Reveal That CTNS Mutations Can Alter Renal Proximal Tubule Differentiation.
Clinical and genetic characteristics of Tunisian children with infantile nephropathic cystinosis.
Title: Clinical and genetic characteristics of Tunisian children with infantile nephropathic cystinosis.
Cystinosis and two rare mutations in CTNS gene: two case reports.
Title: Cystinosis and two rare mutations in CTNS gene: two case reports.
Molecular characterization of CTNS mutations in Tunisian patients with ocular cystinosis.
Title: Molecular characterization of CTNS mutations in Tunisian patients with ocular cystinosis.
Hematopoietic Stem Cell Gene Therapy for Cystinosis: From Bench-to-Bedside.
Title: Hematopoietic Stem Cell Gene Therapy for Cystinosis: From Bench-to-Bedside.
Cystinosis induced by CTNS gene mutation: a rare disease study.", trans "CTNS.
Title: Cystinosis induced by CTNS gene mutation: a rare disease study.
Response to Cysteamine in Osteoclasts Obtained from Patients with Nephropathic Cystinosis: A Genotype/Phenotype Correlation.
Title: Response to Cysteamine in Osteoclasts Obtained from Patients with Nephropathic Cystinosis: A Genotype/Phenotype Correlation.
Assessing the integrity of auditory processing and sensory memory in adults with cystinosis (CTNS gene mutations).
Title: Assessing the integrity of auditory processing and sensory memory in adults with cystinosis (CTNS gene mutations).
We present a case of ocular cystinosis caused by two potentially severe CTNS gene mutations. The lack of renal involvement may be due to localised (ocular) aberrant CTNS RNA splicing.
Title: A case of ocular cystinosis associated with two potentially severe CTNS mutations.

Submit: New GeneRIF Correction See all GeneRIFs (51)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Juvenile nephropathic cystinosis MedGen: C0268626 OMIM: 219900 GeneReviews: Cystinosis	Compare labs
Nephropathic cystinosis MedGen: C2931187 OMIM: 219800 GeneReviews: Cystinosis	Compare labs
Ocular cystinosis MedGen: C2931013 OMIM: 219750 GeneReviews: Cystinosis	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

CTNS_4653 (e-PCR)
- UniSTS:462848

A008L05 (e-PCR)
- UniSTS:42768

D10S275 (e-PCR)
- UniSTS:147992

RH36905 (e-PCR)
- UniSTS:87932

D17S829 (e-PCR)
- UniSTS:36008

RH80740 (e-PCR)
- UniSTS:91068

RH92559 (e-PCR)
- UniSTS:85467

D15S1258 (e-PCR)
- UniSTS:26100

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-cystine transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables L-cystine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables L-cystine transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables L-cystine transmembrane transporter activity	NAS Non-traceable Author Statement more info	PubMed
enables L-cystine transmembrane transporter activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables solute:proton symporter activity	IDA Inferred from Direct Assay more info	PubMed

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
acts_upstream_of_or_within L-cystine transport	IDA Inferred from Direct Assay more info	PubMed
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 D-glucose absorption	IEA Inferred from Electronic Annotation more info
involved_in renal albumin 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 more info	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 more info	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	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cystinosin

Names: cystinosis nephropathic

NCBI Reference Sequences (RefSeq)

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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

NG_012489.2 RefSeqGene

Range

5293..31636

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001031681.3 → NP_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:125 → 357

2A43; Lysosomal Cystine Transporter
NM_001374492.1 → NP_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:125 → 357

2A43; Lysosomal Cystine Transporter
NM_001374493.1 → NP_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:1 → 210

2A43; Lysosomal Cystine Transporter
NM_001374494.1 → NP_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:1 → 210

2A43; Lysosomal Cystine Transporter
NM_001374495.1 → NP_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:1 → 210

2A43; Lysosomal Cystine Transporter
NM_001374496.1 → NP_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:1 → 210

2A43; Lysosomal Cystine Transporter
NM_004937.3 → NP_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:125 → 357

2A43; Lysosomal Cystine Transporter

pfam04193
Location:128 → 185

PQ-loop; PQ loop repeat