Juvenile neuronal ceroid lipofuscinosis: genes and variants
Juvenile neuronal ceroid lipofuscinosis is linked to 1 analyzed protein (CLN3). 7 DNA variants are known to cause it; 4 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Juvenile neuronal ceroid lipofuscinosis
CLN3: Battenin
It participates in lysosomal and endosomal homeostasis, membrane trafficking, and cellular lipid handling, although its complete molecular role remains unresolved. Biallelic loss-of-function variants cause juvenile neuronal ceroid lipofuscinosis, with progressive vision loss, epilepsy, cognitive decline, and motor impairment.
7 disease-causing and 4 uncertain variants in CLN3 are linked to Juvenile neuronal ceroid lipofuscinosis.
Where Juvenile neuronal ceroid lipofuscinosis variants cluster
- CLN3 Lumenal (positions 299–346): 4 of 7 disease-causing changes, 5.2× more than its size predicts.
Known disease-causing variants in Juvenile neuronal ceroid lipofuscinosis
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| CLN3 V330F | 330 | Lumenal | Disease-causing (★★) |
| CLN3 R334C | 334 | Lumenal | Disease-causing (★★) |
| CLN3 V330I | 330 | Lumenal | Disease-causing (★★) |
| CLN3 R334H | 334 | Lumenal | Disease-causing (★★) |
| CLN3 M1I | 1 | Cytoplasmic | Disease-causing (★★) |
| CLN3 E295K | 295 | Transmembrane | Disease-causing (★★) |
| CLN3 R405W | 405 | Cytoplasmic | Disease-causing (★★) |
Same protein, different disease
- Neuronal ceroid lipofuscinosis is also caused by CLN3 variants; they fall mostly in different places as the Juvenile neuronal ceroid lipofuscinosis variants (19 disease-causing).
Diseases related to Juvenile neuronal ceroid lipofuscinosis
- Retinitis pigmentosa, also linked to CLN3
- Neuronal ceroid lipofuscinosis, also linked to CLN3
Frequently asked questions
Which genes are linked to Juvenile neuronal ceroid lipofuscinosis?
In CATVariant, Juvenile neuronal ceroid lipofuscinosis is linked to 1 analyzed protein: CLN3 (Battenin).
How many genetic variants are linked to Juvenile neuronal ceroid lipofuscinosis?
12 variants: 7 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 4 are of uncertain significance or have conflicting reports.
Which uncertain variants in Juvenile neuronal ceroid lipofuscinosis look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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