CLN5 Type Neuronal Ceroid Lipofuscinosis (CLN5-NCL)

CLN5 Type Neuronal Ceroid Lipofuscinosis, often abbreviated as CLN5-NCL, is a rare inherited neurodegenerative disorder. It primarily affects children and belongs to a larger group of disorders called neuronal ceroid lipofuscinoses (NCLs), which are collectively referred to as Batten disease. CLN5-NCL is classified as a lysosomal storage disorder, meaning it arises from dysfunction in the lysosomes, the intracellular organelles responsible for breaking down and recycling unwanted cellular material. When lysosomes fail to function properly, cellular waste accumulates, leading to progressive damage to nerve cells and, over time, widespread neurodegeneration.

Overview

CLN5

The onset of CLN5-NCL typically occurs in early childhood, with the first signs often appearing between four and seven years of age. In some cases, symptoms may appear earlier or develop later, depending on the specific mutation and other genetic or environmental factors. The earliest manifestations are often subtle and may be mistaken for typical developmental variation. These include clumsiness or delays in motor coordination and speech. Over time, the condition progresses, leading to a cascade of neurological problems such as vision loss, seizures, ataxia, and significant cognitive decline. This progressive course results in loss of independence and increasing disability. Although there is currently no cure, advances in research are driving the development of experimental therapies, particularly gene-based interventions, which hold promise for altering the natural course of the disease.

Genetic Basis and Protein Function

Genomic Location and Gene Function

The CLN5 gene, located on the long arm of chromosome 13 in the 13q22.3 region, encodes a soluble lysosomal glycoprotein. This protein plays a central role in maintaining the health of lysosomes, which function as the “cleaning systems” of cells by breaking down waste and recycling essential components. Although CLN5 was initially believed to be a membrane-bound protein, it is now understood that the protein undergoes processing by proteases, transforming it into a soluble form that performs critical functions inside lysosomes.

Functional Role of the CLN5 Protein

The CLN5 protein does not act in isolation. It interacts with other NCL-related proteins such as CLN1, CLN2, CLN3, CLN6, and CLN8, as well as proteins involved in intracellular transport pathways, including sortilin and Rab7. These interactions are essential for maintaining lysosomal homeostasis and ensuring proper protein trafficking within the cell. When the CLN5 protein is absent or dysfunctional, this balance is disrupted, leading to the accumulation of toxic by-products. Over time, these changes impair the health of neurons, eventually causing cell death and progressive neurodegeneration.

Disorder Classification

Mutations in the CLN5 gene give rise to Neuronal Ceroid Lipofuscinosis Type 5, also known as the Finnish variant late-infantile NCL (vLINCL). This alternate name reflects the fact that the disease is significantly more prevalent in Finland compared to other parts of the world.

Epidemiology

CLN5-NCL is considered an ultra-rare condition, meaning that it affects very few individuals worldwide. In Finland, the incidence is approximately 4.8 per 100,000 births, a figure much higher than in other populations. Globally, the estimated incidence ranges from one to three cases per 100,000 individuals. Among the many subtypes of NCL, which range from CLN1 to CLN14, CLN5-NCL is one of the less common forms.

Etiology

The condition follows an autosomal recessive pattern of inheritance, meaning that affected individuals inherit two defective copies of the CLN5 gene, one from each parent. Parents who carry only a single mutated copy are typically healthy carriers but have a 25% chance with each pregnancy of passing the condition to their child. Over fifty pathogenic variants of the CLN5 gene have been documented, including missense mutations, which result in single amino acid substitutions; nonsense mutations, which create premature stop signals during protein synthesis; and frameshift mutations, which disrupt the protein structure entirely. One particular mutation, known as Y392 (previously labeled Y343), is the most commonly observed variant in Finnish patients.

Key Roles of CLN5 in the Cell

The CLN5 protein supports multiple critical cellular processes. It plays a role in S-depalmitoylation, a process that regulates how proteins attach to and detach from cell membranes, ensuring they reach their correct destinations. It also participates in lipid metabolism within lysosomes, including the synthesis of BMP (bis(monoacylglycero)phosphate), a lipid crucial for lysosomal membrane integrity. Additionally, CLN5 is involved in the transport and recycling of lysosomal enzymes, ensuring that these enzymes are delivered where they are needed. Finally, it facilitates communication between organelles, particularly between lysosomes and mitochondria, which is essential for maintaining overall cellular balance. Disruption of these processes in neurons explains the progressive cell death and the neurological decline observed in affected individuals.

Symptoms

The clinical picture of CLN5-NCL reflects its gradual but relentless progression. Early signs often involve motor difficulties such as clumsiness, unsteady gait, or difficulty coordinating movements. These are followed by muscle weakness that worsens as the disease advances. Cognitive symptoms soon become apparent, beginning with delayed language development and learning difficulties in early childhood. Over time, this evolves into a more global cognitive decline resembling dementia.

Vision loss is a defining feature of the disease. Retinal degeneration gradually erodes visual function, often leading to complete blindness during adolescence. Seizures are another prominent symptom, frequently involving generalized episodes and myoclonic jerks, and may become increasingly difficult to control. Behavioral changes such as irritability, emotional instability, and social withdrawal often develop, reflecting the disease’s impact on both neurological and psychological functioning. Sleep disturbances, including difficulty falling asleep and frequent nighttime awakenings, are also common and can exacerbate seizures and overall disease burden.

By the mid-teen years, most patients have lost independent mobility, and blindness is typically complete, underscoring the aggressive nature of the disease.

Testing and Diagnosis

Accurate diagnosis of CLN5-NCL involves a combination of clinical evaluation, imaging studies, laboratory analyses, and genetic testing. Clinicians typically begin with a detailed assessment of developmental history and clinical presentation, particularly when developmental regression, vision loss, or refractory seizures raise suspicion for an NCL disorder. Brain MRI often reveals atrophy of the cerebral cortex and cerebellum, alongside abnormal white matter signals.

Biopsy samples from skin or conjunctival tissue provide another diagnostic clue. Under electron microscopy, these samples show characteristic patterns of autofluorescent lipopigment accumulation, often with fingerprint-like or granular structures. However, genetic testing is the gold standard for diagnosis. Next-generation sequencing (NGS) can identify mutations in the CLN5 gene, providing definitive confirmation. Experimental approaches, such as measuring enzyme activity in patient-derived cells or using induced pluripotent stem cell (iPSC) models to study functional defects, are being explored but are not yet widely used in clinical practice.

Treatment and Management

There is currently no therapy that can reverse or halt the progression of CLN5-NCL. Management therefore focuses on controlling symptoms and maintaining quality of life for as long as possible. Seizure control is a priority; medications such as valproic acid, benzodiazepines, and levetiracetam are commonly prescribed, while drugs like phenytoin and vigabatrin are avoided because they may worsen neurological symptoms. For motor difficulties, agents such as baclofen or trihexyphenidyl, and in some cases botulinum toxin, are used to manage spasticity and dystonia. As swallowing becomes more difficult, nutritional support through feeding tubes, such as percutaneous endoscopic gastrostomy (PEG), may be required, alongside respiratory physiotherapy to reduce complications.

Research is ongoing into disease-modifying treatments. Gene therapy has shown particular promise. In animal studies, delivery of the CLN5 gene directly into the brain using adeno-associated virus (AAV9) vectors extended lifespan and preserved motor and visual function in CLN5-deficient sheep. Early administration, before the onset of significant symptoms, appears to yield the best results, and clinical trials in humans are now underway. Substrate reduction therapy, such as the use of miglustat to reduce lipid accumulation in lysosomes, is being studied, although clinical benefits remain to be established. Enzyme replacement therapy (ERT) is a proven approach for CLN2-NCL using cerliponase alfa, but the development of an effective ERT for CLN5 is still in early experimental stages.

Prognosis

CLN5-NCL is a progressive and fatal disorder. The typical age of onset is between four and seven years, with most affected individuals dying between the ages of 13 and 30. There are rare cases of slower progression, but these are exceptions. Early diagnosis, along with coordinated care and support, plays an essential role in improving quality of life and ensuring timely access to emerging experimental treatments.

Helpful Terms

A gene is a segment of DNA that contains the instructions for building proteins, which are the functional components of cells. Mutations in these instructions can lead to abnormal or absent proteins, disrupting normal cell processes. CLN5-NCL is inherited in an autosomal recessive pattern, meaning both parents must pass on a defective copy of the CLN5 gene for their child to develop the disease. Carriers with only one copy typically show no symptoms.

The CLN5 gene produces a protein that maintains lysosomal function and neuronal health. The lysosome, often described as the cell’s “cleaning system,” is responsible for breaking down and recycling cellular waste. Neuronal ceroid lipofuscinosis (NCL) refers to a family of disorders in which waste materials accumulate in the brain and eyes, progressively damaging neurons and other tissues. Batten disease is a commonly used name for these conditions, particularly those with childhood onset.

References

• Malik K, Santucci K, Sremba L, et al. Neuronal Ceroid Lipofuscinoses Overview. 2001 Oct 10 [Updated 2025 May 29]. In: Adam MP, Feldman J, Mirzaa GM, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2025. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1428/.
• Basak, I., Wicky, H.E., McDonald, K.O. et al. A lysosomal enigma CLN5 and its significance in understanding neuronal ceroid lipofuscinosis. Cell. Mol. Life Sci. 78, 4735–4763 (2021). https://doi.org/10.1007/s00018-021-03813-x.
• Simonati, Alessandro, and Ruth E. Williams. ‘Neuronal Ceroid Lipofuscinosis: The Multifaceted Approach to the Clinical Issues, an Overview’. Frontiers in Neurology, vol. 13, Mar. 2022, p. 811686. DOI.org (Crossref), https://doi.org/10.3389/fneur.2022.811686.
• Zhang, Yuheng, et al. ‘Neuronal Ceroid Lipofuscinosis—Concepts, Classification, and Avenues for Therapy’. CNS Neuroscience & Therapeutics, vol. 31, no. 2, Feb. 2025, p. e70261. DOI.org (Crossref), https://doi.org/10.1111/cns.70261.
• Kaminiów, Konrad, et al. ‘Recent Insight into the Genetic Basis, Clinical Features, and Diagnostic Methods for Neuronal Ceroid Lipofuscinosis’. International Journal of Molecular Sciences, vol. 23, no. 10, May 2022, p. 5729. DOI.org (Crossref), https://doi.org/10.3390/ijms23105729.
• Nicolaou, Paschalis. ‘Editorial: Neuronal Ceroid Lipofuscinosis: Molecular Genetics and Epigenetics’. Frontiers in Genetics, vol. 15, June 2024, p. 1430703. DOI.org (Crossref), https://doi.org/10.3389/fgene.2024.1430703.
• Perez G, Barber GP, Benet-Pages A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Raney BJ, Speir ML, van Baren MJ, Vaske CJ, Haussler D, Kent WJ, Haeussler M. The UCSC Genome Browser database: 2025 update. Nucleic Acids Res. 2025 Jan 6;53(D1):D1243-D1249. doi: 10.1093/nar/gkae974. PMID: 39460617; PMCID: PMC11701590.

キーワード｜Keywords

^{CLN5, 神経セロイドリポフスチン症, バッテン病, リソソーム病, 常染色体劣性, 13q22.3, 自家蛍光性色素, 発達退行, ミオクローヌス, 運動失調, 視力障害, てんかん, 遺伝子治療, AAV9, 酵素補充療法, 神経変性, リソソーム機能障害, 自食作用（オートファジー）, BMP合成酵素, Rab7, sortilin, 網膜変性, ミクログリア, 酸化ストレス, 脂質代謝, 発達遅延}