CLN3 encodes CLN3 lysosomal/endosomal transmembrane protein, battenin (438 aa). Mediates microtubule-dependent, anterograde transport connecting the Golgi network, endosomes, autophagosomes, lysosomes and plasma membrane, and participates in several cellular processes such as regulation of lysosomal pH, lysosome protein degradation, receptor-mediated endocytosis, autophagy, transport of proteins and lipids from the TGN, apoptosis and synaptic transmission. Highest expression in Thyroid (26.1 TPM) and Colon Transverse (22.6 TPM).

Neuronal ceroid lipofuscinosis 3 is associated with mutations in the CLN3 gene on chromosome 16.

The CLN3 protein participates in CLN3 transports GalCer to plasma membrane pathway.

CLN3 is classified as a druggable target (Transporter category) with score 0.0.

Genetic testing for CLN3 is available. Testing is considered confirmatory for diagnosis.

Biomarker and diagnostic research for neuronal ceroid lipofuscinosis 3 has been reported in the published literature.

No approved treatments are currently available for neuronal ceroid lipofuscinosis 3. An additional 1 compound holds orphan drug designation.

Orphan Drug Designations

While no drugs are FDA-approved specifically for neuronal ceroid lipofuscinosis 3, some of the following designated compounds may be used off-label in clinical practice. Treatment decisions should be made in consultation with a specialist familiar with this condition.

The following drugs have received orphan drug designation from the FDA for neuronal ceroid lipofuscinosis 3. Orphan designation reflects regulatory interest and does not indicate approval for treatment.

Gene therapy approaches for neuronal ceroid lipofuscinosis 3 have been reported in the published literature.

Phenotype severity distribution: 9 always present features.

Estimated prevalence: <1 in 1,000,000 (VERY_RARE).

2 clinical trials registered, 1 recruiting. Interventions under study include other interventions and gene therapy. Pipeline includes 1 PHASE1. Research is sponsored by a mix of industry and academic institutions.

101 publications have been identified in PubMed for neuronal ceroid lipofuscinosis 3. Research spans Basic Science / Preclinical (34%), Case Report / Case Series (18%), and Epidemiology / Natural History (14%).

Recent Publications

• Ding Y (2026). [PMID: 42282513](https://pubmed.ncbi.nlm.nih.gov/42282513/). *bioRxiv*. [Basic Science / Preclinical]

• Wani MA (2026). [PMID: 42163273](https://pubmed.ncbi.nlm.nih.gov/42163273/). *J Transl Med*. [Basic Science / Preclinical]

• Chandra S (2026). [PMID: 42146023](https://pubmed.ncbi.nlm.nih.gov/42146023/). *NeuroImmune Pharm Ther*. [Gene Therapy / Novel Therapeutics]

• Mink JW (2026). [PMID: 41808212](https://pubmed.ncbi.nlm.nih.gov/41808212/). *Orphanet J Rare Dis*. [Review / Meta-Analysis]

• Gokalp S (2026). [PMID: 42100905](https://pubmed.ncbi.nlm.nih.gov/42100905/). *Clin Dysmorphol*. [Case Report / Case Series]

• Auvin S (2026). [PMID: 41354011](https://pubmed.ncbi.nlm.nih.gov/41354011/). *European journal of paediatric neurology : EJPN : official journal of the European Paediatric Neurology Society*. [Epidemiology / Natural History]

• Liu K (2026). [PMID: 41986128](https://pubmed.ncbi.nlm.nih.gov/41986128/). *Zhonghua yi xue za zhi*. [Diagnostic / Biomarker]

• Barnes M (2026). [PMID: 41741265](https://pubmed.ncbi.nlm.nih.gov/41741265/). *Trends in pharmacological sciences*. [Review / Meta-Analysis]

• Simonati A (2026). [PMID: 40708162](https://pubmed.ncbi.nlm.nih.gov/40708162/). *Developmental medicine and child neurology*. [Basic Science / Preclinical]

• Whiteman IT (2026). [PMID: 41501856](https://pubmed.ncbi.nlm.nih.gov/41501856/). *Orphanet journal of rare diseases*. [Basic Science / Preclinical]