CLN3 Gene: Batten Disease Ceroid-Lipofuscinosis Neuronal 3
Genetic insights into CLN3, a key player in neuronal ceroid lipofuscinosis and lysosomal function.
Gene Information Card
| Symbol | CLN3 |
|---|---|
| Full Name | CLN3 lysosomal/endosomal transmembrane protein, battenin |
| Gene Type | protein coding |
| Chromosomal Location | 16p11.2 |
| NCBI Gene ID | 1201 ncbi.nlm.nih.gov/gene/1201 |
| Ensembl ID | ENSG00000171862 |
| UniProt ID | Q13286 |
| OMIM ID | 607042 |
| HGNC ID | 2074 |
| Aliases | BTS, JNCL, Batten disease, ceroid-lipofuscinosis neuronal 3 |
Description
The CLN3 gene encodes battenin, a transmembrane protein primarily localized to lysosomes and endosomes. It is involved in lysosomal pH regulation, autophagy, and intracellular trafficking. Mutations in CLN3 cause juvenile neuronal ceroid lipofuscinosis (Batten disease), a progressive neurodegenerative disorder characterized by accumulation of autofluorescent lipopigments in neurons and other cells.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Juvenile neuronal ceroid lipofuscinosis (Batten disease) | Loss-of-function mutations lead to defective lysosomal function, impaired autophagy, and accumulation of ceroid lipofuscin. | ClinVar, OMIM |
| Retinitis pigmentosa (isolated) | Some CLN3 variants may cause retinal degeneration without full neurological symptoms. | ClinVar, literature |
| Neuronal ceroid lipofuscinosis (other forms) | Compound heterozygous mutations can present with atypical phenotypes. | OMIM, ClinVar |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 10.2 | Medium |
| Testis | 8.5 | Medium |
| Kidney | 7.8 | Low |
| Liver | 6.1 | Low |
| Heart | 5.4 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| SH-SY5Y (neuroblastoma) | 12.3 | High expression; used in neuronal studies |
| HeLa | 8.7 | Moderate expression |
| HEK293 | 7.9 | Moderate expression |
| HepG2 | 5.2 | Low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.462_463del (p.Gly154GlufsTer38) | Frameshift | Most common in Northern European populations (~70% of alleles) | Loss of function; truncated protein |
| c.1054C>T (p.Arg352Trp) | Missense | Rare | Likely loss of function; altered protein stability |
| c.791_792del (p.Phe264LeufsTer18) | Frameshift | Rare | Loss of function; premature stop |
| c.1A>G (p.Met1?) | Start codon loss | Very rare | Loss of function; no protein synthesis |
Mutation functional classification
Loss of Function (LOF)
Most CLN3 mutations are loss-of-function, leading to reduced or absent battenin protein, causing lysosomal dysfunction and neurodegeneration.
Gain of Function (GOF)
No evidence of gain-of-function mutations for CLN3.
Dominant Negative (DN)
Not reported; CLN3 disease is autosomal recessive, so dominant-negative effects are unlikely.
View complete mutation data：
Gene Ontology (GO)
| • lysosomal membrane | • endosome membrane |
| • protein binding | • identical protein binding |
| • autophagy | • lysosomal pH regulation |
| • intracellular protein transport | • response to oxidative stress |
Pathways
• Lysosomal degradation pathway
• Autophagy pathway
• mTOR signaling (indirect)
• Endosomal sorting complex required for transport (ESCRT) pathway (interaction)
Protein Summary
Battenin (CLN3) is a 438-amino acid transmembrane protein with six predicted transmembrane domains. It localizes to lysosomes and endosomes, where it regulates pH and vesicular trafficking. It interacts with proteins such as Hook1 and CTSD (cathepsin D). Defects in battenin lead to accumulation of subunit c of mitochondrial ATP synthase and other autofluorescent materials, characteristic of Batten disease.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| CLN3 Knockout HEK293 Cell Line | EDJ-KQ4292 | Human | 1201 | Details Get a Quote |
| CLN3 Knockout HeLa Cell Line | EDJ-KQ18209 | Human | 1201 | Details Get a Quote |
| CLN3 Knockout HCT 116 Cell Line | EDJ-KQ25483 | Human | 1201 | Details Get a Quote |
| CLN3 Knockout A-549 Cell Line | EDJ-KQ26780 | Human | 1201 | Details Get a Quote |
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