• Gene id: 1201

Gene Summary

• Gene Symbol: CLN3   Gene   UCSC   Ensembl
• Aliases: BTN1, BTS, JNCL
• Gene name: CLN3 lysosomal/endosomal transmembrane protein, battenin
• Alternate names: battenin, CLN3, battenin, batten disease protein, ceroid-lipofuscinosis, neuronal 3,
• Gene location: 16p12.1 (28492081: 28466652)     Exons: 16     NC_000016.10
• Gene summary(Entrez): 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
• OMIM: 606015

Protein Summary

• Protein general information: Q13286  
  • Name: Battenin (Batten disease protein) (Protein CLN3)
  • Length: 438  
  • Mass: 47623
  • Tissue specificity: Expressed in the cortical brain, pancreas, spleen, and testis with weaker expression in the peripheral nerve (at protein level). Highly expressed in gray matter (at protein level). {ECO
• Sequence:

  MGGCAGSRRRFSDSEGEETVPEPRLPLLDHQGAHWKNAVGFWLLGLCNNFSYVVMLSAAHDILSHKRTSGNQSHV
  DPGPTPIPHNSSSRFDCNSVSTAAVLLADILPTLVIKLLAPLGLHLLPYSPRVLVSGICAAGSFVLVAFSHSVGT
  SLCGVVFASISSGLGEVTFLSLTAFYPRAVISWWSSGTGGAGLLGALSYLGLTQAGLSPQQTLLSMLGIPALLLA
  SYFLLLTSPEAQDPGGEEEAESAARQPLIRTEAPESKPGSSSSLSLRERWTVFKGLLWYIVPLVVVYFAEYFINQ
  GLFELLFFWNTSLSHAQQYRWYQMLYQAGVFASRSSLRCCRIRFTWALALLQCLNLVFLLADVWFGFLPSIYLVF
  LIILYEGLLGGAAYVNTFHNIALETSDEHREFAMAATCISDTLGISLSGLLALPLHDFLCQLS

• Structural information:
  • Interpro: IPR003492  IPR018460  IPR036259  
  • STRING: ENSP00000454229
• Other Databases: GeneCards:  CLN3  Malacards:  CLN3

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0007040	lysosome organization	IBA	biological process
GO:0005773	vacuole	IBA	cellular component
GO:0005764	lysosome	IBA	cellular component
GO:0051453	regulation of intracellular pH	IBA	biological process
GO:0015809	arginine transport	IBA	biological process
GO:0007042	lysosomal lumen acidification	IBA	biological process
GO:0055037	recycling endosome	IDA	cellular component
GO:0005764	lysosome	IDA	cellular component
GO:0005770	late endosome	IDA	cellular component
GO:0005764	lysosome	IDA	cellular component
GO:0005794	Golgi apparatus	IDA	cellular component
GO:0005802	trans-Golgi network	IDA	cellular component
GO:0005764	lysosome	IDA	cellular component
GO:0005765	lysosomal membrane	IDA	cellular component
GO:0051861	glycolipid binding	IDA	molecular function
GO:0005764	lysosome	IDA	cellular component
GO:0005770	late endosome	IDA	cellular component
GO:0120146	sulfatide binding	IDA	molecular function
GO:0005770	late endosome	IDA	cellular component
GO:0047496	vesicle transport along microtubule	IMP	biological process
GO:0005765	lysosomal membrane	IMP	cellular component
GO:0106049	regulation of cellular response to osmotic stress	IMP	biological process
GO:0045121	membrane raft	IMP	cellular component
GO:0005901	caveola	IMP	cellular component
GO:0031901	early endosome membrane	IMP	cellular component
GO:0005765	lysosomal membrane	IMP	cellular component
GO:0005794	Golgi apparatus	IMP	cellular component
GO:0070613	regulation of protein processing	IMP	biological process
GO:0032228	regulation of synaptic transmission, GABAergic	ISS	biological process
GO:0007611	learning or memory	ISS	biological process
GO:0044754	autolysosome	ISS	cellular component
GO:0036359	renal potassium excretion	ISS	biological process
GO:0046836	glycolipid transport	IMP	biological process
GO:0043066	negative regulation of apoptotic process	ISS	biological process
GO:0005764	lysosome	IMP	cellular component
GO:0051493	regulation of cytoskeleton organization	IMP	biological process
GO:1901096	regulation of autophagosome maturation	ISS	biological process
GO:0090384	phagosome-lysosome docking	ISS	biological process
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005770	late endosome	IMP	cellular component
GO:0046474	glycerophospholipid biosynthetic process	IMP	biological process
GO:0005515	protein binding	IPI	molecular function
GO:1905162	regulation of phagosome maturation	ISS	biological process
GO:0005515	protein binding	IPI	molecular function
GO:2001288	positive regulation of caveolin-mediated endocytosis	ISS	biological process
GO:0044857	plasma membrane raft organization	ISS	biological process
GO:0042998	positive regulation of Golgi to plasma membrane protein transport	ISS	biological process
GO:0048549	positive regulation of pinocytosis	ISS	biological process
GO:0051966	regulation of synaptic transmission, glutamatergic	ISS	biological process
GO:0005515	protein binding	IPI	molecular function
GO:1905244	regulation of modification of synaptic structure	ISS	biological process
GO:0048172	regulation of short-term neuronal synaptic plasticity	ISS	biological process
GO:0009992	cellular water homeostasis	ISS	biological process
GO:1903076	regulation of protein localization to plasma membrane	ISS	biological process
GO:1905146	lysosomal protein catabolic process	ISS	biological process
GO:0005886	plasma membrane	IMP	cellular component
GO:1900079	regulation of arginine biosynthetic process	ISS	biological process
GO:0010762	regulation of fibroblast migration	IMP	biological process
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0061909	autophagosome-lysosome fusion	ISS	biological process
GO:0090385	phagosome-lysosome fusion	ISS	biological process
GO:0090160	Golgi to lysosome transport	IMP	biological process
GO:0016020	membrane	IEA	cellular component
GO:0030054	cell junction	IEA	cellular component
GO:0005794	Golgi apparatus	IEA	cellular component
GO:0005764	lysosome	IEA	cellular component
GO:0043005	neuron projection	IEA	cellular component
GO:0031410	cytoplasmic vesicle	IEA	cellular component
GO:0005768	endosome	IEA	cellular component
GO:0005886	plasma membrane	IEA	cellular component
GO:0016020	membrane	IEA	cellular component
GO:0016021	integral component of membrane	IEA	cellular component
GO:0045202	synapse	IEA	cellular component
GO:0005515	protein binding	IPI	molecular function
GO:0005764	lysosome	IEA	cellular component
GO:0031902	late endosome membrane	IEA	cellular component
GO:0043005	neuron projection	IEA	cellular component
GO:0005794	Golgi apparatus	IEA	cellular component
GO:0005901	caveola	IEA	cellular component
GO:0005765	lysosomal membrane	IEA	cellular component
GO:0031901	early endosome membrane	IEA	cellular component
GO:0005795	Golgi stack	IEA	cellular component
GO:0055037	recycling endosome	IEA	cellular component
GO:0000139	Golgi membrane	IEA	cellular component
GO:0045121	membrane raft	IEA	cellular component
GO:0005770	late endosome	IEA	cellular component
GO:0005886	plasma membrane	IEA	cellular component
GO:0005776	autophagosome	IEA	cellular component
GO:0005829	cytosol	IEA	cellular component
GO:0042987	amyloid precursor protein catabolic process	IDA	biological process
GO:0008021	synaptic vesicle	IDA	cellular component
GO:0005901	caveola	IDA	cellular component
GO:0005802	trans-Golgi network	IDA	cellular component
GO:0005794	Golgi apparatus	IDA	cellular component
GO:0005783	endoplasmic reticulum	IDA	cellular component
GO:0005764	lysosome	IDA	cellular component
GO:0000139	Golgi membrane	IDA	cellular component
GO:0016021	integral component of membrane	IDA	cellular component
GO:0005886	plasma membrane	IDA	cellular component
GO:0005737	cytoplasm	IDA	cellular component
GO:0045121	membrane raft	IDA	cellular component
GO:0043005	neuron projection	IDA	cellular component
GO:0035752	lysosomal lumen pH elevation	IDA	biological process
GO:0030176	integral component of endoplasmic reticulum membrane	IDA	cellular component
GO:0008021	synaptic vesicle	IDA	cellular component
GO:0005795	Golgi stack	IDA	cellular component
GO:0005765	lysosomal membrane	IDA	cellular component
GO:0000139	Golgi membrane	IDA	cellular component
GO:0015809	arginine transport	IDA	biological process
GO:0005886	plasma membrane	IDA	cellular component
GO:0005769	early endosome	IDA	cellular component
GO:0005634	nucleus	IDA	cellular component
GO:0061024	membrane organization	ISS	biological process
GO:0043066	negative regulation of apoptotic process	IMP	biological process
GO:0016485	protein processing	ISS	biological process
GO:0007040	lysosome organization	ISS	biological process
GO:0005765	lysosomal membrane	HDA	cellular component
GO:0043524	negative regulation of neuron apoptotic process	ISS	biological process
GO:0042133	neurotransmitter metabolic process	ISS	biological process
GO:0035235	ionotropic glutamate receptor signaling pathway	ISS	biological process
GO:0007042	lysosomal lumen acidification	IMP	biological process
GO:0005776	autophagosome	ISS	cellular component
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0097352	autophagosome maturation	ISS	biological process
GO:0051480	regulation of cytosolic calcium ion concentration	ISS	biological process
GO:0050885	neuromuscular process controlling balance	ISS	biological process
GO:0043086	negative regulation of catalytic activity	ISS	biological process
GO:0001508	action potential	ISS	biological process
GO:0045861	negative regulation of proteolysis	ISS	biological process
GO:0008306	associative learning	ISS	biological process
GO:0006898	receptor-mediated endocytosis	IMP	biological process
GO:0005770	late endosome	ISS	cellular component
GO:0007040	lysosome organization	IBA	biological process
GO:0005773	vacuole	IBA	cellular component
GO:0005764	lysosome	IBA	cellular component
GO:0051453	regulation of intracellular pH	IBA	biological process
GO:0015809	arginine transport	IBA	biological process
GO:0007042	lysosomal lumen acidification	IBA	biological process
GO:0055037	recycling endosome	IDA	cellular component
GO:0005764	lysosome	IDA	cellular component
GO:0005770	late endosome	IDA	cellular component
GO:0005764	lysosome	IDA	cellular component
GO:0005794	Golgi apparatus	IDA	cellular component
GO:0005802	trans-Golgi network	IDA	cellular component
GO:0005764	lysosome	IDA	cellular component
GO:0005765	lysosomal membrane	IDA	cellular component
GO:0051861	glycolipid binding	IDA	molecular function
GO:0005764	lysosome	IDA	cellular component
GO:0005770	late endosome	IDA	cellular component
GO:0120146	sulfatide binding	IDA	molecular function
GO:0005770	late endosome	IDA	cellular component
GO:0047496	vesicle transport along microtubule	IMP	biological process
GO:0005765	lysosomal membrane	IMP	cellular component
GO:0106049	regulation of cellular response to osmotic stress	IMP	biological process
GO:0045121	membrane raft	IMP	cellular component
GO:0005901	caveola	IMP	cellular component
GO:0031901	early endosome membrane	IMP	cellular component
GO:0005765	lysosomal membrane	IMP	cellular component
GO:0005794	Golgi apparatus	IMP	cellular component
GO:0070613	regulation of protein processing	IMP	biological process
GO:0032228	regulation of synaptic transmission, GABAergic	ISS	biological process
GO:0007611	learning or memory	ISS	biological process
GO:0044754	autolysosome	ISS	cellular component
GO:0036359	renal potassium excretion	ISS	biological process
GO:0046836	glycolipid transport	IMP	biological process
GO:0043066	negative regulation of apoptotic process	ISS	biological process
GO:0005764	lysosome	IMP	cellular component
GO:0051493	regulation of cytoskeleton organization	IMP	biological process
GO:1901096	regulation of autophagosome maturation	ISS	biological process
GO:0090384	phagosome-lysosome docking	ISS	biological process
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005770	late endosome	IMP	cellular component
GO:0046474	glycerophospholipid biosynthetic process	IMP	biological process
GO:0005515	protein binding	IPI	molecular function
GO:1905162	regulation of phagosome maturation	ISS	biological process
GO:0005515	protein binding	IPI	molecular function
GO:2001288	positive regulation of caveolin-mediated endocytosis	ISS	biological process
GO:0044857	plasma membrane raft organization	ISS	biological process
GO:0042998	positive regulation of Golgi to plasma membrane protein transport	ISS	biological process
GO:0048549	positive regulation of pinocytosis	ISS	biological process
GO:0051966	regulation of synaptic transmission, glutamatergic	ISS	biological process
GO:0005515	protein binding	IPI	molecular function
GO:1905244	regulation of modification of synaptic structure	ISS	biological process
GO:0048172	regulation of short-term neuronal synaptic plasticity	ISS	biological process
GO:0009992	cellular water homeostasis	ISS	biological process
GO:1903076	regulation of protein localization to plasma membrane	ISS	biological process
GO:1905146	lysosomal protein catabolic process	ISS	biological process
GO:0005886	plasma membrane	IMP	cellular component
GO:1900079	regulation of arginine biosynthetic process	ISS	biological process
GO:0010762	regulation of fibroblast migration	IMP	biological process
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0061909	autophagosome-lysosome fusion	ISS	biological process
GO:0090385	phagosome-lysosome fusion	ISS	biological process
GO:0090160	Golgi to lysosome transport	IMP	biological process
GO:0016020	membrane	IEA	cellular component
GO:0030054	cell junction	IEA	cellular component
GO:0005794	Golgi apparatus	IEA	cellular component
GO:0005764	lysosome	IEA	cellular component
GO:0043005	neuron projection	IEA	cellular component
GO:0031410	cytoplasmic vesicle	IEA	cellular component
GO:0005768	endosome	IEA	cellular component
GO:0005886	plasma membrane	IEA	cellular component
GO:0016020	membrane	IEA	cellular component
GO:0016021	integral component of membrane	IEA	cellular component
GO:0045202	synapse	IEA	cellular component
GO:0005515	protein binding	IPI	molecular function
GO:0005764	lysosome	IEA	cellular component
GO:0031902	late endosome membrane	IEA	cellular component
GO:0043005	neuron projection	IEA	cellular component
GO:0005794	Golgi apparatus	IEA	cellular component
GO:0005901	caveola	IEA	cellular component
GO:0005765	lysosomal membrane	IEA	cellular component
GO:0031901	early endosome membrane	IEA	cellular component
GO:0005795	Golgi stack	IEA	cellular component
GO:0055037	recycling endosome	IEA	cellular component
GO:0000139	Golgi membrane	IEA	cellular component
GO:0045121	membrane raft	IEA	cellular component
GO:0005770	late endosome	IEA	cellular component
GO:0005886	plasma membrane	IEA	cellular component
GO:0005776	autophagosome	IEA	cellular component
GO:0005829	cytosol	IEA	cellular component
GO:0042987	amyloid precursor protein catabolic process	IDA	biological process
GO:0008021	synaptic vesicle	IDA	cellular component
GO:0005901	caveola	IDA	cellular component
GO:0005802	trans-Golgi network	IDA	cellular component
GO:0005794	Golgi apparatus	IDA	cellular component
GO:0005783	endoplasmic reticulum	IDA	cellular component
GO:0005764	lysosome	IDA	cellular component
GO:0000139	Golgi membrane	IDA	cellular component
GO:0016021	integral component of membrane	IDA	cellular component
GO:0005886	plasma membrane	IDA	cellular component
GO:0005737	cytoplasm	IDA	cellular component
GO:0045121	membrane raft	IDA	cellular component
GO:0043005	neuron projection	IDA	cellular component
GO:0035752	lysosomal lumen pH elevation	IDA	biological process
GO:0030176	integral component of endoplasmic reticulum membrane	IDA	cellular component
GO:0008021	synaptic vesicle	IDA	cellular component
GO:0005795	Golgi stack	IDA	cellular component
GO:0005765	lysosomal membrane	IDA	cellular component
GO:0000139	Golgi membrane	IDA	cellular component
GO:0015809	arginine transport	IDA	biological process
GO:0005886	plasma membrane	IDA	cellular component
GO:0005769	early endosome	IDA	cellular component
GO:0005634	nucleus	IDA	cellular component
GO:0061024	membrane organization	ISS	biological process
GO:0043066	negative regulation of apoptotic process	IMP	biological process
GO:0016485	protein processing	ISS	biological process
GO:0007040	lysosome organization	ISS	biological process
GO:0005765	lysosomal membrane	HDA	cellular component
GO:0043524	negative regulation of neuron apoptotic process	ISS	biological process
GO:0042133	neurotransmitter metabolic process	ISS	biological process
GO:0035235	ionotropic glutamate receptor signaling pathway	ISS	biological process
GO:0007042	lysosomal lumen acidification	IMP	biological process
GO:0005776	autophagosome	ISS	cellular component
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0097352	autophagosome maturation	ISS	biological process
GO:0051480	regulation of cytosolic calcium ion concentration	ISS	biological process
GO:0050885	neuromuscular process controlling balance	ISS	biological process
GO:0043086	negative regulation of catalytic activity	ISS	biological process
GO:0001508	action potential	ISS	biological process
GO:0045861	negative regulation of proteolysis	ISS	biological process
GO:0008306	associative learning	ISS	biological process
GO:0006898	receptor-mediated endocytosis	IMP	biological process
GO:0005770	late endosome	ISS	cellular component

KEGG pathways

Pathway id	Pathway name
hsa04142	Lysosome

Diseases

Associated diseases	References
Neuronal ceroid lipofuscinosis	KEGG:H00149
Batten disease	KEGG:H02275
Neuronal ceroid lipofuscinosis	KEGG:H00149
Batten disease	KEGG:H02275
Aberrant CpGs in Low Motility Sperm	MIK: 21674046
Spermatogenic defects	MIK: 31037746

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
21674046	Aberrant CpGs in Low Motility Sperm			18	Male infertility	GSE26881
31037746	Spermatogenic defects			28 men with azoospermia	Male infertility	Microarray