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CLN6 gene

CLN6 transmembrane ER protein

Normal Function

The CLN6 gene provides instructions for making a protein whose function is not well understood. Within cells, the CLN6 protein is found in a structure called the endoplasmic reticulum, which is involved in protein processing and transport. Research suggests that the CLN6 protein regulates the transportation of certain proteins and fats from the endoplasmic reticulum to lysosomes. Lysosomes are compartments in the cell that digest and recycle materials. Based on this function, the CLN6 protein appears to help cells get rid of materials they no longer need.

Health Conditions Related to Genetic Changes

CLN6 disease

More than 70 mutations in the CLN6 gene have been found to cause CLN6 disease. This condition impairs motor and mental development, typically starting in early to late childhood, causing gradually worsening problems with movement and a decline in intellectual function. In some cases, signs and symptoms of CLN6 disease do not appear until adulthood.

Most CLN6 gene mutations result in the production of an abnormal CLN6 protein that is quickly broken down (degraded). As a result, there is a severe reduction in the amount of functional CLN6 protein in cells. While it is not known how the loss of this protein causes the signs and symptoms of CLN6 disease, it is likely that the protein's quick degradation contributes to the childhood onset of CLN6 disease.

In the cases in which CLN6 disease develops in adulthood, CLN6 gene mutations often change single protein building blocks (amino acids), resulting in a CLN6 protein with reduced function. Research suggests that these CLN6 gene mutations allow enough functional protein to be produced so that signs and symptoms of the disorder do not develop until later in life.

CLN6 disease is characterized by the accumulation of proteins or peptides and other substances in lysosomes. These accumulations occur in cells throughout the body; however, nerve cells seem to be particularly vulnerable to their effects. The accumulations can cause cell damage leading to cell death. The progressive death of nerve cells in the brain and other tissues leads to the signs and symptoms of CLN6 disease. However, it is unclear how mutations in the CLN6 gene are involved in the buildup of substances in lysosomes in CLN6 disease. These accumulations occur in more cells throughout the body in children with CLN6 disease than in affected adults.

More About This Health Condition

Other Names for This Gene

  • ceroid-lipofuscinosis neuronal protein 6
  • ceroid-lipofuscinosis, neuronal 6, late infantile, variant
  • CLN4A
  • FLJ20561
  • HsT18960
  • nclf

Additional Information & Resources

Tests Listed in the Genetic Testing Registry

Scientific Articles on PubMed

Catalog of Genes and Diseases from OMIM

Gene and Variant Databases


  • Arsov T, Smith KR, Damiano J, Franceschetti S, Canafoglia L, Bromhead CJ, Andermann E, Vears DF, Cossette P, Rajagopalan S, McDougall A, Sofia V, Farrell M, Aguglia U, Zini A, Meletti S, Morbin M, Mullen S, Andermann F, Mole SE, Bahlo M, Berkovic SF. Kufs disease, the major adult form of neuronal ceroid lipofuscinosis, caused by mutations in CLN6. Am J Hum Genet. 2011 May 13;88(5):566-73. doi: 10.1016/j.ajhg.2011.04.004. Epub 2011 May 5. Citation on PubMed or Free article on PubMed Central
  • Canafoglia L, Gilioli I, Invernizzi F, Sofia V, Fugnanesi V, Morbin M, Chiapparini L, Granata T, Binelli S, Scaioli V, Garavaglia B, Nardocci N, Berkovic SF, Franceschetti S. Electroclinical spectrum of the neuronal ceroid lipofuscinoses associated with CLN6 mutations. Neurology. 2015 Jul 28;85(4):316-24. doi: 10.1212/WNL.0000000000001784. Epub 2015 Jun 26. Citation on PubMed or Free article on PubMed Central
  • Cannelli N, Garavaglia B, Simonati A, Aiello C, Barzaghi C, Pezzini F, Cilio MR, Biancheri R, Morbin M, Dalla Bernardina B, Granata T, Tessa A, Invernizzi F, Pessagno A, Boldrini R, Zibordi F, Grazian L, Claps D, Carrozzo R, Mole SE, Nardocci N, Santorelli FM. Variant late infantile ceroid lipofuscinoses associated with novel mutations in CLN6. Biochem Biophys Res Commun. 2009 Feb 20;379(4):892-7. doi: 10.1016/j.bbrc.2008.12.159. Epub 2009 Jan 7. Citation on PubMed
  • Kay C. Same gene, surprising difference: adult neuronal ceroid lipofuscinosis linked to CLN6, mutated in variant late-infantile form. Clin Genet. 2011 Dec;80(6):505-6. doi: 10.1111/j.1399-0004.2011.01761.x. Epub 2011 Aug 30. No abstract available. Citation on PubMed
  • Kurze AK, Galliciotti G, Heine C, Mole SE, Quitsch A, Braulke T. Pathogenic mutations cause rapid degradation of lysosomal storage disease-related membrane protein CLN6. Hum Mutat. 2010 Feb;31(2):E1163-74. doi: 10.1002/humu.21184. Citation on PubMed
  • Sato R, Inui T, Endo W, Okubo Y, Takezawa Y, Anzai M, Morita H, Saitsu H, Matsumoto N, Haginoya K. First Japanese variant of late infantile neuronal ceroid lipofuscinosis caused by novel CLN6 mutations. Brain Dev. 2016 Oct;38(9):852-6. doi: 10.1016/j.braindev.2016.04.007. Epub 2016 May 7. Citation on PubMed

The information on this site should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health.