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Gene

CLN3

CLN3 lysosomal/endosomal transmembrane protein, battenin

Summary

Cytogenetic location
16p12.1
Coordinates
Chromosome 16: 28,477,279–28,492,074 (GRCh38)
Exons
16 exons across 14.8 kb
Protein
438 amino acids
Inheritance
Autosomal recessive
Also known as
BTN1, JNCL, SLC29B1
Previous symbols
BTS
MANE Select transcript
ENST00000636147.2NM_001042432.2
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

    • 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 CLN3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where CLN3 sits. CLN3 and 24 genes near it on chromosome 16, from 27,984,677 to 28,984,676.Chromosome 1616p12.1p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.328 Mb28.2 Mb28.4 Mb28.6 Mb28.8 MbGSG1L: 27,787,526–28,063,754, reverse strandGSG1LXPO6: 28,097,976–28,212,065, reverse strandXPO6SBK1: 28,259,246–28,323,849, forward strandSBK1NPIPB6: 28,342,517–28,363,508, reverse strandNPIPB6EIF3CL: 28,376,676–28,403,851, reverse strandEIF3CLNPIPB7: 28,456,322–28,472,336, reverse strandNPIPB7: 28,456,371–28,492,098, reverse strandCLN3: 28,477,279–28,492,074, reverse strandCLN3APOBR: 28,494,635–28,498,964, forward strandAPOBRIL27: 28,499,360–28,512,051, reverse strandNUPR1: 28,532,708–28,539,068, reverse strandNUPR1SGF29: 28,538,176–28,591,792, forward strandSGF29SULT1A2: 28,589,688–28,599,913, reverse strandSULT1A2SULT1A1: 28,604,997–28,612,503, reverse strandSULT1A1NPIPB8: 28,637,654–28,658,744, forward strandNPIPB8EIF3C: 28,688,558–28,745,938, forward strandEIF3CNPIPB9: 28,751,787–28,772,864, forward strandNPIPB9ATXN2L: 28,822,983–28,837,237, forward strandATXN2LTUFM: 28,841,618–28,846,419, reverse strandTUFMSH2B1: 28,846,584–28,875,103, forward strandSH2B1ATP2A1: 28,878,383–28,904,511, forward strandATP2A1RABEP2: 28,898,740–28,936,526, reverse strandRABEP2CD19: 28,931,965–28,939,342, forward strandCD19NFATC2IP: 28,950,807–28,967,092, forward strandNFATC2IPSPNS1: 28,974,126–28,984,548, forward strandSPNS1Diagram of CLN3: 16 exons on the reverse strand of chromosome 16Exon 16: 7 known disease-causing sitesExon 15: 4 known disease-causing sitesExon 14: 13 known disease-causing sitesExon 13: 8 known disease-causing sitesExon 12: 9 known disease-causing sitesExon 11: 6 known disease-causing sitesExon 10: 10 known disease-causing sitesExon 9: 18 known disease-causing sitesExon 8: 10 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 6: 8 known disease-causing sitesExon 5: 7 known disease-causing sitesExon 4: 10 known disease-causing sitesExon 3: 5 known disease-causing sitesExon 2: 5 known disease-causing sitesExon 16: 28,477,279–28,477,635, 357 basesExon 15: 28,477,737–28,477,877, 141 basesExon 14: 28,482,105–28,482,198, 94 basesExon 13: 28,482,327–28,482,382, 56 basesExon 12: 28,482,477–28,482,545, 69 basesExon 11: 28,482,626–28,482,672, 47 basesExon 10: 28,484,006–28,484,118, 113 basesExon 9: 28,486,347–28,486,490, 144 basesExon 8: 28,486,578–28,486,650, 73 basesExon 7: 28,487,456–28,487,541, 86 basesExon 6: 28,487,662–28,487,741, 80 basesExon 5: 28,488,591–28,488,662, 72 basesExon 4: 28,489,290–28,489,386, 97 basesExon 3: 28,491,482–28,491,560, 79 basesExon 2: 28,491,714–28,491,835, 122 basesExon 1: 28,492,020–28,492,074, 55 bases16141210864215′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 1.7 kb of the gene's 14.8 kb; 1,317 of those bases code for the protein.

How a genome test reads CLN3

173

positions in CLN3 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 14.8 kb of CLN3, introns included, not only the 1.7 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.). CLN3 gene: CLN3 lysosomal/endosomal transmembrane protein, battenin. Retrieved 17 October 2026, from https://dantelabs.com/genes/cln3

Vancouver

Dante Labs. CLN3 gene: CLN3 lysosomal/endosomal transmembrane protein, battenin [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cln3

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