CLN3 is commonly referred to as Juvenile Neuronal Ceroid Lipofuscinosis (JNCL) or Juvenile Batten disease. 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.The consortium used exon amplification of a cosmid that contained D16S298, which yielded a candidate gene that was disrupted by a 1-kb genomic deletion in all patients carrying the 56 chromosome. Three separate deletions and a point mutation altering a splice site in 3 unrelated families confirmed the candidate as the CLN3 gene. The disease gene encodes a deduced 438-amino acid protein.