Protein detail

CLN3

Battenin (Batten disease protein) (Protein CLN3)

Entry name CLN3	UniProt ID Q13286	EVMP confidence score 0.38
Supporting publications (n) 8	Transmembrane count 6	Protein classification Disease related genesHuman disease related genesPotential drug targetsPredicted intracellular proteinsPredicted membrane proteinsTransporters

EVMP confidence score

Annotation confidence score; open for threshold definitions.

Extremely high >= 0.85High >= 0.70Medium >= 0.55Low >= 0.40

Basic Information13

Protein Names

Battenin (Batten disease protein) (Protein CLN3)

Protein Class (6)

Disease related genesHuman disease related genesPotential drug targetsPredicted intracellular proteinsPredicted membrane proteinsTransporters

Protein Function (6)

Predicted intracellular proteins
Human disease related genes:Congenital disorders of metabolism:Congenital disorders of lipid/glycolipid metabolism
Potential drug targets
Transporters:Electrochemical Potential-driven transporters
Disease related genes
Human disease related genes:Congenital disorders of metabolism:Lysosomal storage diseases

Transmembrane

38..58; Helical; 128..148; Helical; 152..172; Helical; 183..203; Helical; 278..298; Helical; 347..367; Helical

Transmembrane Count

Ensembl

ENSG00000188603

Entrez Gene Symbol

CLN3

Gene Synonym (3)

BTN1BTSJNCL

Gene Description

CLN3 lysosomal/endosomal transmembrane protein, battenin

Chromosome

Position

28474111-28495575

Supporting publications (n)

EVMP confidence score

0.38

Fluorescence & Localization5

Tissue Specificbone marrowCell SpecificPlateletsSingle-Nuclei Brain Specificcentral nervous system macrophageBlood Cell SpecificbasophilBlood Lineage Specificgranulocytes

Function & Pathway7

Protein Function (6)

Predicted intracellular proteins
Human disease related genes:Congenital disorders of metabolism:Congenital disorders of lipid/glycolipid metabolism
Potential drug targets
Transporters:Electrochemical Potential-driven transporters
Disease related genes
Human disease related genes:Congenital disorders of metabolism:Lysosomal storage diseases

Cellular Component (24)

Page 1 of 3

Molecular Function (5)

Biological Process (3)

KEGG

hsa04142 Lysosome biogenesis

Reactome (2)

Mediation Categories (6)

Adhesion and uptake mediationClinical-translation mediationFusion and delivery mediationImmune mediationMetabolism mediationReceptor-signaling mediation

Relations & Evidence20

Ligand-Receptor Signaling (17)

17 records.

Category	Parent	Database	Transmitter	Receiver	Secreted	Plasma Membrane (Transmembrane)	Plasma Membrane (Peripheral)
transmembrane	transmembrane	Ramilowski_location	No	No	No	No	No
transmembrane	transmembrane	OmniPath	No	No	No	No	No
plasma_membrane	plasma_membrane	UniProt_location	No	No	No	No	No
plasma_membrane	plasma_membrane	OmniPath	No	No	No	No	No
cell_surface	cell_surface	Surfaceome	No	No	No	No	No
cell_surface	cell_surface	OmniPath	No	No	No	No	No
transmembrane	transmembrane_predicted	Phobius	No	No	No	No	No

Page 2 of 2Previous

Regulatory Interaction Network (1)

1 record.

Source Protein Symbol	Source UniProt ID	Target Protein Symbol	Target UniProt ID	Is Directed	Is Stimulation	Is Inhibition	Database	References
CDK1	P06493	CLN3	Q13286	Yes	No	Yes	SIGNOR	SIGNOR:23217712

Protein Complex Composition (1)

1 record.

Component Name	Component Gene Symbols	Component UniProt ID	Stoichiometry	Database	Database IDs	References
	CLN3 GLE1 NUP107 NUP133 NUP155 NUP205 NUP214 NUP93 NUP98 NXF1 RAE1 SEH1L UBC	O75694 P0CG48 P35658 P52948 P57740 P78406 Q13286 Q53GS7 Q8N1F7 Q8WUM0 Q92621 Q96EE3 Q9UBU9	1:1:1:1:1:1:1:1:1:1:1:1:1	NetworkBlastCompleat	Compleat:HC7755

Isolation & Detection Technology (1)

1 record.

EV Isolation Method	Detection Method	Number of References	References
Protein Organic Solvent Precipitation	R SequencingMass spectrometry	1	32384937

Sequence, Structure & Domains10

Sequences

Length

438

Mass

47,623

Sequence

MGGCAGSRRRFSDSEGEETVPEPRLPLLDHQGAHWKNAVGFWLLGLCNNFSYVVMLSAAHDILSHKRTSGNQSHVDPGPTPIPHNSSSRFDCNSVSTAAVLLADILPTLVIKLLAPLGLHLLPYSPRVLVSGICAAGSFVLVAFSHSVGTSLCGVVFASISSGLGEVTFLSLTAFYPRAVISWWSSGTGGAGLLGALSYLGLTQAGLSPQQTLLSMLGIPALLLASYFLLLTSPEAQDPGGEEEAESAARQPLIRTEAPESKPGSSSSLSLRERWTVFKGLLWYIVPLVVVYFAEYFINQGLFELLFFWNTSLSHAQQYRWYQMLYQAGVFASRSSLRCCRIRFTWALALLQCLNLVFLLADVWFGFLPSIYLVFLIILYEGLLGGAAYVNTFHNIALETSDEHREFAMAATCISDTLGISLSGLLALPLHDFLCQLS

Alternative Products

Event=Alternative splicing; Named isoforms=7; Comment=Additional isoforms seem to exist.; Name=1; IsoId=Q13286-1; Sequence=Displayed; Name=2; IsoId=Q13286-2; Sequence=VSP_004166; Name=3; IsoId=Q13286-3; Sequence=VSP_004167; Name=4; IsoId=Q13286-4; Sequence=VSP_004168; Name=5; IsoId=Q13286-5; Sequence=VSP_004169, VSP_004170; Name=6; IsoId=Q13286-6; Sequence=VSP_047631, VSP_047632; Name=7; IsoId=Q13286-7; Sequence=VSP_057347

Alternative Sequence

75..98; Missing (in isoform 7); 99..127; AVLLADILPTLVIKLLAPLGLHLLPYSPR -> PPGSRQWDLCCWKLRPGCLFSFCGDQPVC (in isoform 6); 128..226; Missing (in isoform 6); 155..264; Missing (in isoform 5); 178..225; Missing (in isoform 2); 280..302; GLLWYIVPLVVVYFAEYFINQGL -> VRMMAG (in isoform 3); 322..438; Missing (in isoform 4); 353..438; CLNLVFLLADVWFGFLPSIYLVFLIILYEGLLGGAAYVNTFHNIALETSDEHREFAMAATCISDTLGISLSGLLALPLHDFLCQLS -> MESRSVAQAGM (in isoform 5)

Domain & Motif Annotations

Motif

242..244; Lysosomal targeting motif; 253..254; Lysosomal targeting motif. Required for AP1G1, AP2A2 and AP3D1 interaction; 409..419; Lysosomal targeting motif

Domain (CC)

The C-terminal (153-438) mediates KCNIP3 interaction and the cytoprotective activity (PubMed:17189291). the dileucine motif mediates AP1G1 and AP3D1 interaction (PubMed:15598649).

Region

1..25; Disordered; 237..268; Disordered

Protein Families

Battenin family

Sequence Similarities

Belongs to the battenin family.

Clinical Relevance4

Disease Involvement (3)

Disease variantNeurodegenerationNeuronal ceroid lipofuscinosis

Related Diseases

Lysosomal disease

Biomarker

Phase 1/2

Antibody

HPA063280

Supporting Publications8

PMID	Title	Abstract
27894104	Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers.	No abstract available
29045505	Surfaceome profiling enables isolation of cancer-specific exosomal cargo in liquid biopsies from pancreatic cancer patients.	Proteomic analysis of the exosome 'surfaceome' revealed multiple PDAC-specific biomarker candidates: CLDN4, EPCAM, CD151, LGALS3BP, HIST2H2BE, and HIST2H2BF. Droplet digital PCR was used on 74 patients (136 total exosome samples) to determine baseline KRAS mutation call rates while patients were on therapy. KRAS mutations in total exosomes were detected in 44.1% of patients undergoing active therapy compared with 73.0% following exosome capture using the selected biomarkers.
30408591	Portrait of blood-derived extracellular vesicles in patients with Parkinson's disease.	No abstract available
30950185	Unique Protein Profiles of Extracellular Vesicles as Diagnostic Biomarkers for Early and Advanced Non-Small Cell Lung Cancer.	No abstract available
33204424	Proteomic analysis of extracellular vesicles reveals an immunogenic cargo in rheumatoid arthritis synovial fluid.	No abstract available
34817906	Proteomic dissection of large extracellular vesicle surfaceome unravels interactive surface platform.	No abstract available
38168906	Defining the relationship between cellular and extracellular vesicle (EV) content in breast cancer via an integrative multi-omic analysis.	No abstract available
39558134	Serum small extracellular vesicles-derived BST2 as a biomarker for papillary thyroid microcarcinoma promotes lymph node metastasis.	No abstract available