CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLN3provided by HGNC
Official Full Name: CLN3 lysosomal/endosomal transmembrane protein, batteninprovided by HGNC
Primary source: HGNC:HGNC:2074
See related: Ensembl:ENSG00000188603 MIM:607042; AllianceGenome:HGNC:2074
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BTS; BTN1; JNCL
Summary: 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]
Expression: Ubiquitous expression in placenta (RPKM 23.0), colon (RPKM 17.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p12.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (28466653..28492082, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (28903667..28920379) , (28747320..28747572, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (28477974..28503403, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of CLN3 in microglia leads to impaired lipid metabolism and myelin turnover.
Title: Loss of CLN3 in microglia leads to impaired lipid metabolism and myelin turnover.
CLN3 transcript complexity revealed by long-read RNA sequencing analysis.
Title: CLN3 transcript complexity revealed by long-read RNA sequencing analysis.
TRPML1 activation ameliorates lysosomal phenotypes in CLN3 deficient retinal pigment epithelial cells.
Title: TRPML1 activation ameliorates lysosomal phenotypes in CLN3 deficient retinal pigment epithelial cells.
CLN3 deficiency leads to neurological and metabolic perturbations during early development.
Title: CLN3 deficiency leads to neurological and metabolic perturbations during early development.
Loss of the batten disease protein CLN3 leads to mis-trafficking of M6PR and defective autophagic-lysosomal reformation.
Title: Loss of the batten disease protein CLN3 leads to mis-trafficking of M6PR and defective autophagic-lysosomal reformation.
The Batten disease protein CLN3 is important for stress granules dynamics and translational activity.
Title: The Batten disease protein CLN3 is important for stress granules dynamics and translational activity.
CLN3 is required for the clearance of glycerophosphodiesters from lysosomes.
Title: CLN3 is required for the clearance of glycerophosphodiesters from lysosomes.
Converging roles of PSENEN/PEN2 and CLN3 in the autophagy-lysosome system.
Title: Converging roles of PSENEN/PEN2 and CLN3 in the autophagy-lysosome system.
A diagnostic confidence scheme for CLN3 disease.
Title: A diagnostic confidence scheme for CLN3 disease.
Gene correction of the CLN3 c.175G>A variant in patient-derived induced pluripotent stem cells prevents pathological changes in retinal organoids.
Title: Gene correction of the CLN3 c.175G>A variant in patient-derived induced pluripotent stem cells prevents pathological changes in retinal organoids.

Submit: New GeneRIF Correction See all GeneRIFs (77)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neuronal ceroid lipofuscinosis 3 MedGen: C0751383 OMIM: 204200 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Common variants at five new loci associated with early-onset inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of ceroid-lipofuscinosis, neuronal 3 (CLN3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Genome-wide shRNA screening identifies CLN3, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_4175-4176:996679465:3 (e-PCR)
- UniSTS:269341

D16S2668 (e-PCR)
- UniSTS:152417

D16S3212 (e-PCR)
- UniSTS:38243

RH70509 (e-PCR)
- UniSTS:90988

D1S1423 (e-PCR)
- UniSTS:149619

D16S298 (e-PCR)
- UniSTS:78504

D16S3081 (e-PCR)
- UniSTS:26553

D16S298 (e-PCR)
- UniSTS:149709

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium-dependent protein binding	IEA Inferred from Electronic Annotation more info
enables glycolipid binding	IDA Inferred from Direct Assay more info	PubMed
enables glycolipid transfer activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sulfatide binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in L-arginine transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in actin cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in action potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in amyloid precursor protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in associative learning	ISS Inferred from Sequence or Structural Similarity more info
involved_in autophagosome maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in autophagosome-lysosome fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in blood vessel endothelial cell migration	IEA Inferred from Electronic Annotation more info
involved_in ceramide transport	TAS Traceable Author Statement more info
involved_in glycerophospholipid biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glycolipid transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular water homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in ionotropic glutamate receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in learning or memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in lysosomal lumen acidification	IBA Inferred from Biological aspect of Ancestor more info
involved_in lysosomal lumen acidification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lysosomal lumen pH elevation	IDA Inferred from Direct Assay more info	PubMed
involved_in lysosomal protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in lysosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in lysosome organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in membrane organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of neuron apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of proteolysis	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuromuscular process controlling balance	ISS Inferred from Sequence or Structural Similarity more info
involved_in phagosome-lysosome docking	ISS Inferred from Sequence or Structural Similarity more info
involved_in phagosome-lysosome fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in plasma membrane raft organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of Golgi to plasma membrane protein transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of caveolin-mediated endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of pinocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to plasma membrane	IEA Inferred from Electronic Annotation more info
involved_in protein processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of arginine biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of autophagosome maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of autophagosome size	IEA Inferred from Electronic Annotation more info
involved_in regulation of cellular response to osmotic stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cytosolic calcium ion concentration	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of fibroblast migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of filopodium assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of modification of synaptic structure	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of phagosome maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of protein localization to plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of protein processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of short-term neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic transmission, GABAergic	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic transmission, glutamatergic	ISS Inferred from Sequence or Structural Similarity more info
involved_in renal potassium excretion	ISS Inferred from Sequence or Structural Similarity more info
involved_in vesicle transport along microtubule	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	IMP Inferred from Mutant Phenotype more info	PubMed
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in Golgi stack	IDA Inferred from Direct Assay more info	PubMed
located_in autolysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in autophagosome	ISS Inferred from Sequence or Structural Similarity more info
located_in caveola	IDA Inferred from Direct Assay more info	PubMed
located_in caveola	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IMP Inferred from Mutant Phenotype more info	PubMed
located_in late endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in lysosome	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane raft	IDA Inferred from Direct Assay more info	PubMed
located_in membrane raft	IMP Inferred from Mutant Phenotype more info	PubMed
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in recycling endosome	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: battenin

Names: CLN3, battenin; batten disease protein; ceroid-lipofuscinosis, neuronal 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008654.2 RefSeqGene

Range

5001..30650

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_689

mRNA and Protein(s)

NM_000086.2 → NP_000077.1 battenin isoform a

See identical proteins and their annotated locations for NP_000077.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AF077962, AI138575, AU105965, DA869025, U32680

Consensus CDS

CCDS10632.1

UniProtKB/Swiss-Prot

B2R7J1, B4DXL3, O00668, O95089, Q13286, Q549S9, Q9UP09, Q9UP11, Q9UP12, Q9UP13, Q9UP14

UniProtKB/TrEMBL

A0A1B0GWD3

Related

ENSP00000353073.9, ENST00000359984.12

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
NM_001042432.2 → NP_001035897.1 battenin isoform a

See identical proteins and their annotated locations for NP_001035897.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AF077957, AI138575, DA552461, DB101039

Consensus CDS

CCDS10632.1

UniProtKB/Swiss-Prot

B2R7J1, B4DXL3, O00668, O95089, Q13286, Q549S9, Q9UP09, Q9UP11, Q9UP12, Q9UP13, Q9UP14

UniProtKB/TrEMBL

A0A1B0GWD3

Related

ENSP00000490105.1, ENST00000636147.2

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
NM_001286104.2 → NP_001273033.1 battenin isoform b

See identical proteins and their annotated locations for NP_001273033.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AC138894, AK302027, DA703317

Consensus CDS

CCDS73855.1

UniProtKB/TrEMBL

A0A1B0GWD3

Related

ENSP00000353116.3, ENST00000360019.8

Conserved Domains (1) summary

pfam02487
Location:40 → 413

CLN3; CLN3 protein
NM_001286105.2 → NP_001273034.1 battenin isoform c

See identical proteins and their annotated locations for NP_001273034.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks two exons compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (c) with a shorter and distinct N-terminus compared to isoform a.

Source sequence(s)

AC138894, AK297690, AK302027, BP252176

UniProtKB/TrEMBL

B4DMY6, O95086

Conserved Domains (1) summary

pfam02487
Location:27 → 337

CLN3; CLN3 protein
NM_001286109.2 → NP_001273038.1 battenin isoform d

See identical proteins and their annotated locations for NP_001273038.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence, the 3' UTR, and lacks an alternate in-frame exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (d) with a shorter N-terminus and missing an alternate internal segment compared to isoform a.

Source sequence(s)

BC111068, BP252176, DA869025

Consensus CDS

CCDS73853.1

UniProtKB/TrEMBL

O95086, Q2TA70

Conserved Domains (1) summary

pfam02487
Location:1 → 359

CLN3; CLN3 protein
NM_001286110.2 → NP_001273039.1 battenin isoform e

See identical proteins and their annotated locations for NP_001273039.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (e) with a shorter N-terminus and missing an alternate internal segment compared to isoform a.

Source sequence(s)

AC138894, AK294070, BP252176, DA869025

Consensus CDS

CCDS73854.1

UniProtKB/TrEMBL

B4DFF3, H3BPM8, O95086

Related

ENSP00000350523.9, ENST00000357857.14

Conserved Domains (1) summary

pfam02487
Location:1 → 383

CLN3; CLN3 protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

28466653..28492082 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

28747320..28747572 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)
NC_060940.1 Alternate T2T-CHM13v2.0

Range

28903667..28920379

Download

GenBank, FASTA, Sequence Viewer (Graphics)