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Gene

CLN5

CLN5 lysosomal BMP synthase

Summary

Cytogenetic location
13q22.3
Coordinates
Chromosome 13: 76,992,081–77,005,117 (GRCh38)
Exons
4 exons across 13 kb
Protein
358 amino acids
Inheritance
Autosomal recessive
MANE Select transcript
ENST00000377453.9NM_006493.4
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

  • Neuronal Ceroid Lipofuscinosis

    • Late Infantile Neuronal Ceroid LipofuscinosisAutosomal recessive

      A genetically heterogeneous group of neuronal ceroid lipofuscinoses (NCLs) typically characterized by onset during infancy or early childhood with decline of mental and motor capacities, epilepsy, and vision loss through retinal degeneration.

      • 6 GenCC submitters rate it definitive or strong
    • Autosomal recessive

      A group of inherited progressive degenerative brain diseases characterized clinically by a decline of mental and other capacities, epilepsy, and vision loss through retinal degeneration, and histopathologically by intracellular accumulation of an autofluorescent material, ceroid lipofuscin, in the neuronal cells in the brain and in the retina.

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

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 CLN5 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 13, with a bracket where CLN5 sits. CLN5 and 6 genes near it on chromosome 13, from 76,498,599 to 77,498,598.Chromosome 1313q22.3p13p12p11.2p11.1q11q12.11q12.12q12.13q12.2q12.3q13.1q13.2q13.3q14.11q14.12q14.13q14.2q14.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q3476.6 Mb76.8 Mb77 Mb77.2 Mb77.4 MbKCTD12: 76,880,175–76,886,405, reverse strandKCTD12ACOD1: 76,948,511–76,958,638, forward strandACOD1: 76,992,078–77,129,589, forward strandCLN5: 76,992,081–77,005,117, forward strandCLN5FBXL3: 76,992,598–77,027,211, reverse strandFBXL3MYCBP2: 77,042,474–77,327,105, reverse strandMYCBP2: 77,326,905–77,326,988, reverse strandDiagram of CLN5: 4 exons on the forward strand of chromosome 13Exon 1: 21 known disease-causing sitesExon 2: 16 known disease-causing sitesExon 3: 28 known disease-causing sitesExon 4: 64 known disease-causing sitesExon 1: 76,992,081–76,992,271, 191 basesExon 2: 76,995,063–76,995,228, 166 basesExon 3: 76,995,902–76,996,127, 226 basesExon 4: 77,000,458–77,005,117, 4,660 bases12345′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 5.2 kb of the gene's 13 kb; 1,077 of those bases code for the protein.

How a genome test reads CLN5

140

positions in CLN5 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 13 kb of CLN5, introns included, not only the 5.2 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.). CLN5 gene: CLN5 lysosomal BMP synthase. Retrieved 17 October 2026, from https://dantelabs.com/genes/cln5

Vancouver

Dante Labs. CLN5 gene: CLN5 lysosomal BMP synthase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cln5

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