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Protein

Battenin

Gene

CLN3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in microtubule-dependent, anterograde transport of late endosomes and lysosomes.1 Publication

GO - Molecular functioni

  • unfolded protein binding Source: ProtInc

GO - Biological processi

  • action potential Source: UniProtKB
  • amyloid precursor protein catabolic process Source: UniProtKB
  • arginine transport Source: UniProtKB
  • associative learning Source: UniProtKB
  • autophagosome maturation Source: UniProtKB
  • cellular amino acid metabolic process Source: UniProtKB
  • ceramide metabolic process Source: UniProtKB
  • galactosylceramide metabolic process Source: UniProtKB
  • globoside metabolic process Source: UniProtKB
  • glucosylceramide metabolic process Source: UniProtKB
  • ionotropic glutamate receptor signaling pathway Source: UniProtKB
  • lysosomal lumen acidification Source: UniProtKB
  • lysosomal lumen pH elevation Source: UniProtKB
  • lysosome organization Source: UniProtKB
  • macroautophagy Source: UniProtKB
  • membrane organization Source: UniProtKB
  • negative regulation of apoptotic process Source: UniProtKB
  • negative regulation of catalytic activity Source: UniProtKB
  • negative regulation of neuron apoptotic process Source: UniProtKB
  • negative regulation of proteolysis Source: UniProtKB
  • neuromuscular process controlling balance Source: UniProtKB
  • neurotransmitter metabolic process Source: UniProtKB
  • protein catabolic process Source: UniProtKB
  • protein processing Source: UniProtKB
  • receptor-mediated endocytosis Source: UniProtKB
  • regulation of cytosolic calcium ion concentration Source: UniProtKB
  • sphingomyelin metabolic process Source: UniProtKB
  • vacuolar transport Source: GO_Central
  • vesicle transport along microtubule Source: UniProtKB

Keywordsi

Biological processTransport

Protein family/group databases

TCDBi2.A.57.5.8 the equilibrative nucleoside transporter (ent) family

Names & Taxonomyi

Protein namesi
Recommended name:
Battenin
Alternative name(s):
Batten disease protein
Protein CLN3
Gene namesi
Name:CLN3
Synonyms:BTS
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

EuPathDBiHostDB:ENSG00000188603.16
HGNCiHGNC:2074 CLN3
MIMi607042 gene
neXtProtiNX_Q13286

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 37CytoplasmicSequence analysisAdd BLAST37
Transmembranei38 – 58HelicalSequence analysisAdd BLAST21
Topological domaini59 – 127LumenalSequence analysisAdd BLAST69
Transmembranei128 – 148HelicalSequence analysisAdd BLAST21
Topological domaini149 – 151CytoplasmicSequence analysis3
Transmembranei152 – 172HelicalSequence analysisAdd BLAST21
Topological domaini173 – 182LumenalSequence analysis10
Transmembranei183 – 203HelicalSequence analysisAdd BLAST21
Topological domaini204 – 277CytoplasmicSequence analysisAdd BLAST74
Transmembranei278 – 298HelicalSequence analysisAdd BLAST21
Topological domaini299 – 346LumenalSequence analysisAdd BLAST48
Transmembranei347 – 367HelicalSequence analysisAdd BLAST21
Topological domaini368 – 438CytoplasmicSequence analysisAdd BLAST71

Keywords - Cellular componenti

Endosome, Lysosome, Membrane

Pathology & Biotechi

Involvement in diseasei

Ceroid lipofuscinosis, neuronal, 3 (CLN3)4 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of neuronal ceroid lipofuscinosis. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. The hallmark of CLN3 is the ultrastructural pattern of lipopigment with a fingerprint profile, which can have 3 different appearances: pure within a lysosomal residual body; in conjunction with curvilinear or rectilinear profiles; and as a small component within large membrane-bound lysosomal vacuoles. The combination of fingerprint profiles within lysosomal vacuoles is a regular feature of blood lymphocytes from patients with neuronal ceroid lipofuscinosis type 3.
See also OMIM:204200
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_005131101L → P in CLN3. 2 PublicationsCorresponds to variant dbSNP:rs386833714EnsemblClinVar.1
Natural variantiVAR_066892134C → R in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833719EnsemblClinVar.1
Natural variantiVAR_005132170L → P in CLN3. 2 PublicationsCorresponds to variant dbSNP:rs386833727EnsemblClinVar.1
Natural variantiVAR_066893187G → A in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833730EnsemblClinVar.1
Natural variantiVAR_066894189G → R in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833731EnsemblClinVar.1
Natural variantiVAR_005133295E → K in CLN3; the mutant is located to vesicles clustered in a perinuclear region. 4 PublicationsCorresponds to variant dbSNP:rs121434286EnsemblClinVar.1
Natural variantiVAR_005134330V → F in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833744EnsemblClinVar.1
Natural variantiVAR_005135334R → C in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833694EnsemblClinVar.1
Natural variantiVAR_005136334R → H in CLN3. 2 PublicationsCorresponds to variant dbSNP:rs386833695EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Neurodegeneration, Neuronal ceroid lipofuscinosis

Organism-specific databases

DisGeNETi1201
GeneReviewsiCLN3
MalaCardsiCLN3
MIMi204200 phenotype
OpenTargetsiENSG00000188603
ENSG00000261832
Orphaneti228346 CLN3 disease
PharmGKBiPA26601

Polymorphism and mutation databases

BioMutaiCLN3
DMDMi2498243

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000898571 – 435BatteninAdd BLAST435
PropeptideiPRO_0000422290436 – 438Removed in mature formCurated3

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei12PhosphoserineCombined sources1
Modified residuei14PhosphoserineCombined sources1
Glycosylationi71N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi85N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi310N-linked (GlcNAc...) asparagineSequence analysis1
Modified residuei435Cysteine methyl esterCurated1
Lipidationi435S-farnesyl cysteine1 Publication1

Post-translational modificationi

Highly glycosylated.1 Publication
Farnesylation is important for trafficking to lysosomes.1 Publication

Keywords - PTMi

Glycoprotein, Lipoprotein, Methylation, Phosphoprotein, Prenylation

Proteomic databases

PaxDbiQ13286
PeptideAtlasiQ13286
PRIDEiQ13286
ProteomicsDBi59277
59278 [Q13286-2]
59279 [Q13286-3]
59280 [Q13286-4]
59281 [Q13286-5]

PTM databases

iPTMnetiQ13286
PhosphoSitePlusiQ13286
SwissPalmiQ13286

Expressioni

Gene expression databases

BgeeiENSG00000188603
CleanExiHS_CLN3
ExpressionAtlasiQ13286 baseline and differential
GenevisibleiQ13286 HS

Organism-specific databases

HPAiHPA063280

Interactioni

Subunit structurei

Interacts with DCTN1, KIF3A, RAB7A and RILP (PubMed:22261744). Interacts with CLN5 (PubMed:19941651).2 Publications

GO - Molecular functioni

  • unfolded protein binding Source: ProtInc

Protein-protein interaction databases

BioGridi107612, 100 interactors
IntActiQ13286, 36 interactors
STRINGi9606.ENSP00000353073

Structurei

3D structure databases

ProteinModelPortaliQ13286
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the battenin family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3880 Eukaryota
ENOG410XT4Z LUCA
GeneTreeiENSGT00390000003249
HOGENOMiHOG000164765
HOVERGENiHBG017297
InParanoidiQ13286
KOiK12389
OMAiIMLIFPA
OrthoDBiEOG091G07YG
PhylomeDBiQ13286
TreeFamiTF314055

Family and domain databases

InterProiView protein in InterPro
IPR003492 Battenin_disease_Cln3
IPR018460 Battenin_disease_Cln3_subgr
IPR036259 MFS_trans_sf
PANTHERiPTHR10981 PTHR10981, 1 hit
PfamiView protein in Pfam
PF02487 CLN3, 1 hit
PIRSFiPIRSF015974 CLN3_BTN1, 1 hit
PRINTSiPR01315 BATTENIN
SUPFAMiSSF103473 SSF103473, 1 hit

Sequences (7)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 7 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: Q13286-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGGCAGSRRR FSDSEGEETV PEPRLPLLDH QGAHWKNAVG FWLLGLCNNF
60 70 80 90 100
SYVVMLSAAH DILSHKRTSG NQSHVDPGPT PIPHNSSSRF DCNSVSTAAV
110 120 130 140 150
LLADILPTLV IKLLAPLGLH LLPYSPRVLV SGICAAGSFV LVAFSHSVGT
160 170 180 190 200
SLCGVVFASI SSGLGEVTFL SLTAFYPRAV ISWWSSGTGG AGLLGALSYL
210 220 230 240 250
GLTQAGLSPQ QTLLSMLGIP ALLLASYFLL LTSPEAQDPG GEEEAESAAR
260 270 280 290 300
QPLIRTEAPE SKPGSSSSLS LRERWTVFKG LLWYIVPLVV VYFAEYFINQ
310 320 330 340 350
GLFELLFFWN TSLSHAQQYR WYQMLYQAGV FASRSSLRCC RIRFTWALAL
360 370 380 390 400
LQCLNLVFLL ADVWFGFLPS IYLVFLIILY EGLLGGAAYV NTFHNIALET
410 420 430
SDEHREFAMA ATCISDTLGI SLSGLLALPL HDFLCQLS
Length:438
Mass (Da):47,623
Last modified:November 1, 1996 - v1
Checksum:iBE25E973CEEC4FD5
GO
Isoform 2 (identifier: Q13286-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     178-225: Missing.

Show »
Length:390
Mass (Da):42,829
Checksum:i30722C86911C70C0
GO
Isoform 3 (identifier: Q13286-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     280-302: GLLWYIVPLVVVYFAEYFINQGL → VRMMAG

Show »
Length:421
Mass (Da):45,570
Checksum:i503A97EDF8B72CC3
GO
Isoform 4 (identifier: Q13286-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     322-438: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Show »
Length:321
Mass (Da):34,569
Checksum:i482F021A8FF39B63
GO
Isoform 5 (identifier: Q13286-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     155-264: Missing.
     353-438: CLNLVFLLAD...PLHDFLCQLS → MESRSVAQAGM

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Show »
Length:253
Mass (Da):28,016
Checksum:i5FFBAA4622A8DF52
GO
Isoform 6 (identifier: Q13286-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     99-127: AVLLADILPTLVIKLLAPLGLHLLPYSPR → PPGSRQWDLCCWKLRPGCLFSFCGDQPVC
     128-226: Missing.

Show »
Length:339
Mass (Da):37,969
Checksum:iDD2C9A3D0A6B022D
GO
Isoform 7 (identifier: Q13286-7) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     75-98: Missing.

Note: No experimental confirmation available.
Show »
Length:414
Mass (Da):45,155
Checksum:i79C2C41ADB5BAADA
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti259P → L in BAG35838 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_005131101L → P in CLN3. 2 PublicationsCorresponds to variant dbSNP:rs386833714EnsemblClinVar.1
Natural variantiVAR_066892134C → R in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833719EnsemblClinVar.1
Natural variantiVAR_005132170L → P in CLN3. 2 PublicationsCorresponds to variant dbSNP:rs386833727EnsemblClinVar.1
Natural variantiVAR_066893187G → A in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833730EnsemblClinVar.1
Natural variantiVAR_066894189G → R in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833731EnsemblClinVar.1
Natural variantiVAR_005133295E → K in CLN3; the mutant is located to vesicles clustered in a perinuclear region. 4 PublicationsCorresponds to variant dbSNP:rs121434286EnsemblClinVar.1
Natural variantiVAR_005134330V → F in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833744EnsemblClinVar.1
Natural variantiVAR_005135334R → C in CLN3. 1 PublicationCorresponds to variant dbSNP:rs386833694EnsemblClinVar.1
Natural variantiVAR_005136334R → H in CLN3. 2 PublicationsCorresponds to variant dbSNP:rs386833695EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_05734775 – 98Missing in isoform 7. 1 PublicationAdd BLAST24
Alternative sequenceiVSP_04763199 – 127AVLLA…PYSPR → PPGSRQWDLCCWKLRPGCLF SFCGDQPVC in isoform 6. 1 PublicationAdd BLAST29
Alternative sequenceiVSP_047632128 – 226Missing in isoform 6. 1 PublicationAdd BLAST99
Alternative sequenceiVSP_004169155 – 264Missing in isoform 5. 1 PublicationAdd BLAST110
Alternative sequenceiVSP_004166178 – 225Missing in isoform 2. 1 PublicationAdd BLAST48
Alternative sequenceiVSP_004167280 – 302GLLWY…INQGL → VRMMAG in isoform 3. 1 PublicationAdd BLAST23
Alternative sequenceiVSP_004168322 – 438Missing in isoform 4. 1 PublicationAdd BLAST117
Alternative sequenceiVSP_004170353 – 438CLNLV…LCQLS → MESRSVAQAGM in isoform 5. 1 PublicationAdd BLAST86

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U32680 mRNA Translation: AAB51075.1
X99832 Genomic DNA Translation: CAA68148.1
AF015593 mRNA Translation: AAD01555.1
AF015598 mRNA Translation: AAD01560.1
AF077956 mRNA Translation: AAD51478.1
AF077957 mRNA Translation: AAD51479.1
AF077958 mRNA Translation: AAD51480.1
AF077959 mRNA Translation: AAD51481.1
AF077961 mRNA Translation: AAD51483.1
AF077962 mRNA Translation: AAD51484.1
AF077966 mRNA Translation: AAD51488.1
AF077960 mRNA Translation: AAD51482.1
AF077963 mRNA Translation: AAD51485.1
AF077965 mRNA Translation: AAD51487.1
AF077971 mRNA Translation: AAD51493.1
AF077972 mRNA Translation: AAD51494.1
AF078169 mRNA Translation: AAD48543.1
AK302027 mRNA Translation: BAG63425.1
AK313002 mRNA Translation: BAG35838.1
AC002425 Genomic DNA Translation: AAC05337.1
AC002544 Genomic DNA Translation: AAC27430.1
AC138894 Genomic DNA No translation available.
CH471279 Genomic DNA Translation: EAW52281.1
CH471279 Genomic DNA Translation: EAW52286.1
BC002394 mRNA Translation: AAH02394.1
BC004433 mRNA Translation: AAH04433.1
CCDSiCCDS10632.1 [Q13286-1]
CCDS73855.1 [Q13286-7]
PIRiA57219
RefSeqiNP_000077.1, NM_000086.2 [Q13286-1]
NP_001035897.1, NM_001042432.1 [Q13286-1]
NP_001273033.1, NM_001286104.1 [Q13286-7]
NP_001273034.1, NM_001286105.1
UniGeneiHs.534667

Genome annotation databases

EnsembliENST00000333496; ENSP00000329171; ENSG00000188603 [Q13286-7]
ENST00000355477; ENSP00000347660; ENSG00000188603 [Q13286-2]
ENST00000357806; ENSP00000350457; ENSG00000188603 [Q13286-6]
ENST00000359984; ENSP00000353073; ENSG00000188603 [Q13286-1]
ENST00000360019; ENSP00000353116; ENSG00000188603 [Q13286-7]
ENST00000565316; ENSP00000456117; ENSG00000188603 [Q13286-3]
ENST00000569030; ENSP00000454680; ENSG00000188603 [Q13286-5]
ENST00000569430; ENSP00000454229; ENSG00000188603 [Q13286-1]
ENST00000636147; ENSP00000490105; ENSG00000188603 [Q13286-1]
GeneIDi1201
KEGGihsa:1201
UCSCiuc002dpo.4 human [Q13286-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiCLN3_HUMAN
AccessioniPrimary (citable) accession number: Q13286
Secondary accession number(s): B2R7J1
, B4DXL3, O00668, O95089, Q549S9, Q9UP09, Q9UP11, Q9UP12, Q9UP13, Q9UP14
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: June 20, 2018
This is version 172 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

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