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Gene

CTNS

cystinosin, lysosomal cystine transporter

Summary

Cytogenetic location
17p13.2
Coordinates
Chromosome 17: 3,636,760–3,663,103 (GRCh38)
Exons
12 exons across 26.3 kb
Protein
367 amino acids
Inheritance
Autosomal recessive
Also known as
CTNS-LSB, PQLC4, SLC66A4
MANE Select transcript
ENST00000046640.9NM_004937.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Cystinosis

    • Cystinosis (nephropathic, juvenile and ocular forms)Autosomal recessive

      Infantile nephropathic cystinosis causes renal Fanconi syndrome, poor growth and progressive kidney failure; juvenile forms start later, and ocular cystinosis affects only the cornea.

      • ClinGen rates the link definitive
      • 7 GenCC submitters rate it definitive or strong
      What knowing changes

      Lifelong cysteamine treatment, started early, slows kidney decline and protects other organs, and cysteamine eye drops dissolve corneal crystals.

Broader groupings

  • Lysosomal Storage Disease

    • Lysosomal storage disease (other and unspecified types)

      One of 59 genes linked to it

      Covers lysosomal storage diseases without a dedicated report, such as Farber disease and other ASAH1-related disorders, prosaposin (PSAP) deficiencies, multiple sulfatase deficiency, mucopolysaccharidosis types IX and X, and Dorfman-Chanarin disease; inheritance varies by subtype, most often autosomal recessive.

      • ClinGen rates the link definitive
      • 7 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How CTNS is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 17, with a bracket where CTNS sits. CTNS and 27 genes near it on chromosome 17, from 3,149,932 to 4,149,931.Chromosome 1717p13.2p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.33.2 Mb3.4 Mb3.6 Mb3.8 Mb4 MbOR1P1: 3,153,890–3,154,882, reverse strandOR1P1OR1A2: 3,197,519–3,198,448, forward strandOR1A2OR1A1: 3,207,539–3,218,896, forward strandOR1A1OR3A2: 3,276,177–3,386,328, reverse strandOR3A2OR3A1: 3,291,017–3,298,360, reverse strandOR3A1OR1R1: 3,385,930–3,386,874, forward strandOR1R1OR1E1: 3,397,104–3,398,410, reverse strandOR1E1OR3A3: 3,411,370–3,424,070, forward strandOR3A3OR1E2: 3,432,870–3,433,841, reverse strandOR1E2SPATA22: 3,440,011–3,513,852, reverse strandSPATA22ASPA: 3,472,374–3,503,405, forward strandASPATRPV3: 3,510,502–3,557,812, reverse strandTRPV3TRPV1: 3,565,444–3,609,880, reverse strandTRPV1: 3,585,149–3,636,249, reverse strandSHPK: 3,607,433–3,636,637, reverse strandSHPKCTNS: 3,636,760–3,663,103, forward strandCTNSTAX1BP3: 3,659,751–3,668,679, reverse strandTAX1BP3P2RX5-TAX1BP3: 3,663,063–3,696,194, reverse strandP2RX5-TAX1BP3EMC6: 3,668,794–3,672,835, forward strandEMC6P2RX5: 3,669,763–3,696,398, reverse strandITGAE: 3,714,628–3,801,225, reverse strandITGAEHASPIN: 3,723,903–3,726,699, forward strandHASPINNCBP3: 3,802,158–3,846,263, reverse strandNCBP3CAMKK1: 3,860,315–3,894,891, reverse strandCAMKK1P2RX1: 3,896,592–3,916,580, reverse strandP2RX1ATP2A3: 3,923,866–3,964,499, reverse strandATP2A3ZZEF1: 4,004,432–4,143,628, reverse strandZZEF1CYB5D2: 4,143,168–4,188,683, forward strandCYB5D2Diagram of CTNS: 12 exons on the forward strand of chromosome 17Exon 3: 8 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 6: 19 known disease-causing sitesExon 7: 16 known disease-causing sitesExon 8: 14 known disease-causing sitesExon 9: 16 known disease-causing sitesExon 10: 24 known disease-causing sitesExon 11: 13 known disease-causing sitesExon 12: 8 known disease-causing sitesExon 1: 3,636,760–3,636,831, 72 basesExon 2: 3,637,107–3,637,316, 210 basesExon 3: 3,640,188–3,640,267, 80 basesExon 4: 3,647,444–3,647,522, 79 basesExon 5: 3,648,847–3,648,931, 85 basesExon 6: 3,654,998–3,655,101, 104 basesExon 7: 3,655,221–3,655,352, 132 basesExon 8: 3,656,487–3,656,586, 100 basesExon 9: 3,656,676–3,656,795, 120 basesExon 10: 3,658,005–3,658,175, 171 basesExon 11: 3,659,858–3,659,975, 118 basesExon 12: 3,660,236–3,663,103, 2,868 bases1246810125′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 4.1 kb of the gene's 26.3 kb; 1,104 of those bases code for the protein.

How a genome test reads CTNS

163

positions in CTNS where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 26.3 kb of CTNS, introns included, not only the 4.1 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). CTNS gene: cystinosin, lysosomal cystine transporter. Retrieved 16 October 2026, from https://dantelabs.com/genes/ctns

Vancouver

Dante Labs. CTNS gene: cystinosin, lysosomal cystine transporter [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ctns

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