Seroatlas · Human Serome Atlas

CLN3

Battenin

Also known as: BTN1, BTS, CLN3_HUMAN, JNCL

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q13286
Gene
CLN3
Ensembl
ENSG00000188603
Chromosome
16
Canonical length
438 aa
Protein class
Disease related genes, Human disease related genes, Potential drug targets, Predicted intracellular proteins, Predicted membrane proteins, Transporters
Quaternary structure
Homooligomer

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

438 residues, UniProt reviewed canonical sequence.

>Q13286|CLN3
     1  MGGCAGSRRR FSDSEGEETV PEPRLPLLDH QGAHWKNAVG FWLLGLCNNF SYVVMLSAAH
    61  DILSHKRTSG NQSHVDPGPT PIPHNSSSRF DCNSVSTAAV LLADILPTLV IKLLAPLGLH
   121  LLPYSPRVLV SGICAAGSFV LVAFSHSVGT SLCGVVFASI SSGLGEVTFL SLTAFYPRAV
   181  ISWWSSGTGG AGLLGALSYL GLTQAGLSPQ QTLLSMLGIP ALLLASYFLL LTSPEAQDPG
   241  GEEEAESAAR QPLIRTEAPE SKPGSSSSLS LRERWTVFKG LLWYIVPLVV VYFAEYFINQ
   301  GLFELLFFWN TSLSHAQQYR WYQMLYQAGV FASRSSLRCC RIRFTWALAL LQCLNLVFLL
   361  ADVWFGFLPS IYLVFLIILY EGLLGGAAYV NTFHNIALET SDEHREFAMA ATCISDTLGI
   421  SLSGLLALPL HDFLCQLS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLN3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Cell surface
Secreted
No
Transmembrane segments
6
Mean surface accessibility (rSASA)
0.29
Highest tissue expression
39 nTPM

Expression across tissuesHPA

Tissue

  • colon: 39 nTPM
  • placenta: 35 nTPM
  • liver: 33 nTPM
  • adrenal gland: 33 nTPM
  • salivary gland: 33 nTPM
  • stomach: 31 nTPM

Single-cell type

  • microglia: 21 nCPM
  • neutrophils: 17 nCPM
  • oligodendrocytes: 16 nCPM
  • choroid plexus epithelial cells: 14 nCPM
  • oligodendrocyte progenitor cells: 13 nCPM
  • astrocytes: 13 nCPM

Immune cell

  • eosinophil: 99 nTPM
  • plasmacytoid DC: 68 nTPM
  • myeloid DC: 64 nTPM
  • basophil: 64 nTPM
  • classical monocyte: 60 nTPM
  • gdT-cell: 58 nTPM

Brain region

  • choroid plexus: 23 nTPM
  • white matter: 22 nTPM
  • thalamus: 21 nTPM
  • medulla oblongata: 19 nTPM
  • cerebellum: 17 nTPM
  • basal ganglia: 17 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CLN3.

Disease | AllUniProt

Conditions CLN3 is implicated in, by any mechanism.

  • Ceroid lipofuscinosis, neuronal, 3 (CLN3) MIM:204200

Disease | GeneticClinVar

229 pathogenic / likely-pathogenic of 1,231 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.91
gnomAD pLI
0
gnomAD missense Z
-0.15
DepMap mean gene effect
0.07
DepMap dependency class
none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CLN3 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CLN3 as an antibody target. Whether an autoantibody or antibody against CLN3 could matter depends on whether native CLN3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CLN3 is annotated at the cell surface, where native CLN3 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label CLN3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/CLN3. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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