CLN3
Chr 16ARCLN3 lysosomal/endosomal transmembrane protein, battenin
Also known as: BTN1, BTS, JNCL, RP101, SLC29B1
The protein mediates microtubule-dependent transport between cellular compartments including the Golgi, endosomes, lysosomes and plasma membrane, and regulates lysosomal pH, autophagy, and synaptic transmission. Mutations cause neuronal ceroid lipofuscinosis type 3 (CLN3 disease), a form of Batten disease characterized by progressive neurodegeneration, through an autosomal recessive inheritance pattern. Disease results from loss-of-function mutations that disrupt the protein's essential roles in intracellular transport and lysosomal function.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Tolerant to missense variation
Lysosomal membrane protein. Biallelic LOF causes CLN3 disease (juvenile Batten disease). The common 1-kb deletion accounts for most alleles. This is a classic autosomal recessive LOF gene.
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
CLN3 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Study for the Treatment for CLN7 Disease
ACTIVE NOT RECRUITINGGene Therapy for Children With CLN3 Batten Disease
ACTIVE NOT RECRUITINGNatural History of Neuronal Ceroid Lipofuscinosis, Batten's CLN6 Diseae
ACTIVE NOT RECRUITINGExamining Developmental Outcomes of Children Diagnosed With CLN2 Disease
ENROLLING BY INVITATIONLong-Term Follow Up of CLN6 Batten Disease Subjects Following Gene Transfer
ACTIVE NOT RECRUITINGNatural History and Longitudinal Clinical Assessments in NCL / Batten Disease, the International DEM-CHILD Database
RECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
RECRUITINGA First-in-Human, Open-Label, Dose-Escalation Study to Evaluate the Safety and Tolerability of Gene Therapy With TTX-381 for the Ocular Manifestations Associated With Neuronal Ceroid Lipofuscinosis Type 2 (CLN2) Disease
RECRUITINGGene Therapy Study for Children With CLN5 Batten Disease
ACTIVE NOT RECRUITINGInherited Retinal Degenerative Disease Registry
RECRUITINGExternal Resources
Links to major genomics databases and tools