CLN3
Chr 16ARCLN3 lysosomal/endosomal transmembrane protein, battenin
Also known as: BTN1, BTS, JNCL, RP101, SLC29B1
This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
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.1
This gene — mechanism propensity
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.
References
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.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
A 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 RECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
RECRUITINGLong-Term Follow Up of CLN6 Batten Disease Subjects Following Gene Transfer
ACTIVE NOT RECRUITINGStudy for the Treatment for CLN7 Disease
ACTIVE NOT RECRUITINGGene Therapy for Children With CLN3 Batten Disease
ACTIVE NOT RECRUITINGNatural History and Longitudinal Clinical Assessments in NCL / Batten Disease, the International DEM-CHILD Database
RECRUITINGInherited Retinal Degenerative Disease Registry
RECRUITINGExamining Developmental Outcomes of Children Diagnosed With CLN2 Disease
ENROLLING BY INVITATIONNatural History of Neuronal Ceroid Lipofuscinosis, Batten's CLN6 Diseae
ACTIVE NOT RECRUITINGGene Therapy Trial for CLN6 Batten Disease
NOT YET RECRUITINGExternal Resources
Links to major genomics databases and tools