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Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®


Reviewed August 2013

What is the official name of the CLN3 gene?

The official name of this gene is “ceroid-lipofuscinosis, neuronal 3.”

CLN3 is the gene's official symbol. The CLN3 gene is also known by other names, listed below.

What is the normal function of the CLN3 gene?

The CLN3 gene provides instructions for making a protein that is found in the membranes of multiple cellular structures, but whose function is not completely understood. Researchers have proposed several potential functions for the CLN3 protein, including protein transport (trafficking), cell-to-cell communication, and the transmission of chemical signals. The CLN3 protein may also be involved in the organization of the cell's structural framework (cytoskeleton), movement of cell structures, and in the self-destruction of cells (apoptosis). Additionally, the CLN3 protein appears to be important for the normal function of cell structures call lysosomes. Lysosomes are compartments in the cell that normally break down toxic substances and recycle different types of molecules. Researchers propose that the CLN3 protein may help regulate the size and relative acidity (pH) of lysosomes.

How are changes in the CLN3 gene related to health conditions?

juvenile Batten disease - caused by mutations in the CLN3 gene

More than 60 mutations in the CLN3 gene have been identified in people with juvenile Batten disease. Juvenile Batten disease impairs mental and motor development beginning in childhood, causing difficulty with walking, speaking, and intellectual functioning. In addition, affected children often develop recurrent seizures (epilepsy) and vision impairment. The most common mutation that causes this condition deletes about 1,000 DNA building blocks (base pairs) in the CLN3 gene. This mutation, which is usually called the 1 kb deletion, removes a critical part of the gene. The 1 kb deletion disrupts the function of the CLN3 protein, leaving only a small amount of normal activity. It is estimated that more than 90 percent of individuals with juvenile Batten disease caused by CLN3 gene mutations have the 1 kb deletion.

Researchers are working to determine how mutations in the CLN3 gene lead to the characteristic features of juvenile Batten disease. These mutations somehow disrupt the function of lysosomes, resulting in the buildup of fatty substances called lipopigments in these cell structures. These accumulations occur in cells throughout the body, but neurons in the brain seem to be particularly vulnerable to the damage caused by lipopigments. The progressive death of cells, especially in the brain, leads to vision loss, seizures, and intellectual decline in people with juvenile Batten disease.

Where is the CLN3 gene located?

Cytogenetic Location: 16p12.1

Molecular Location on chromosome 16: base pairs 28,466,653 to 28,492,302

(Homo sapiens Annotation Release 107, GRCh38.p2) (NCBI (

The CLN3 gene is located on the short (p) arm of chromosome 16 at position 12.1.

The CLN3 gene is located on the short (p) arm of chromosome 16 at position 12.1.

More precisely, the CLN3 gene is located from base pair 28,466,653 to base pair 28,492,302 on chromosome 16.

See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about CLN3?

You and your healthcare professional may find the following resources about CLN3 helpful.

You may also be interested in these resources, which are designed for genetics professionals and researchers.

What other names do people use for the CLN3 gene or gene products?

  • BTS
  • JNCL
  • MGC102840

See How are genetic conditions and genes named? ( in the Handbook.

What glossary definitions help with understanding CLN3?

acidity ; apoptosis ; cell ; ceroid ; cytoskeleton ; deletion ; DNA ; epilepsy ; gene ; juvenile ; kb ; lipid ; lipofuscin ; motor ; mutation ; pH ; protein ; toxic

You may find definitions for these and many other terms in the Genetics Home Reference Glossary.


  • Isolation of a novel gene underlying Batten disease, CLN3. The International Batten Disease Consortium. Cell. 1995 Sep 22;82(6):949-57. (
  • Kitzmüller C, Haines RL, Codlin S, Cutler DF, Mole SE. A function retained by the common mutant CLN3 protein is responsible for the late onset of juvenile neuronal ceroid lipofuscinosis. Hum Mol Genet. 2008 Jan 15;17(2):303-12. Epub 2007 Oct 18. (
  • Mitchison HM, Taschner PE, Kremmidiotis G, Callen DF, Doggett NA, Lerner TJ, Janes RB, Wallace BA, Munroe PB, O'Rawe AM, Gardiner RM, Mole SE. Structure of the CLN3 gene and predicted structure, location and function of CLN3 protein. Neuropediatrics. 1997 Feb;28(1):12-4. (
  • NCBI Gene (
  • Phillips SN, Benedict JW, Weimer JM, Pearce DA. CLN3, the protein associated with batten disease: structure, function and localization. J Neurosci Res. 2005 Mar 1;79(5):573-83. Review. (
  • Rakheja D, Narayan SB, Bennett MJ. The function of CLN3P, the Batten disease protein. Mol Genet Metab. 2008 Mar;93(3):269-74. Review. Erratum in: Mol Genet Metab. 2008 Jun;94(2):270. (
  • Tuxworth RI, Vivancos V, O'Hare MB, Tear G. Interactions between the juvenile Batten disease gene, CLN3, and the Notch and JNK signalling pathways. Hum Mol Genet. 2009 Feb 15;18(4):667-78. doi: 10.1093/hmg/ddn396. Epub 2008 Nov 21. (
  • Uusi-Rauva K, Kyttälä A, van der Kant R, Vesa J, Tanhuanpää K, Neefjes J, Olkkonen VM, Jalanko A. Neuronal ceroid lipofuscinosis protein CLN3 interacts with motor proteins and modifies location of late endosomal compartments. Cell Mol Life Sci. 2012 Jun;69(12):2075-89. doi: 10.1007/s00018-011-0913-1. Epub 2012 Jan 20. (


The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? ( in the Handbook.

Reviewed: August 2013
Published: February 8, 2016