CLN5 CLN5 intracellular trafficking protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLN5provided by HGNC
Official Full Name: CLN5 intracellular trafficking proteinprovided by HGNC
Primary source: HGNC:HGNC:2076
See related: Ensembl:ENSG00000102805 MIM:608102; AllianceGenome:HGNC:2076
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
Summary: This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function.[provided by RefSeq, Oct 2008]
Expression: Ubiquitous expression in thyroid (RPKM 44.6), kidney (RPKM 19.6) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q22.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (76992081..77005117)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (76215721..76228757)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (77566216..77579252)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

The Batten disease gene product CLN5 is the lysosomal bis(monoacylglycero)phosphate synthase.
Title: The Batten disease gene product CLN5 is the lysosomal bis(monoacylglycero)phosphate synthase.
Lysosomal dysfunction, autophagic defects, and CLN5 accumulation underlie the pathogenesis of KCTD7-mutated neuronal ceroid lipofuscinoses.
Title: Lysosomal dysfunction, autophagic defects, and CLN5 accumulation underlie the pathogenesis of KCTD7-mutated neuronal ceroid lipofuscinoses.
Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration.
Title: Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration.
Deficiency of the Lysosomal Protein CLN5 Alters Lysosomal Function and Movement.
Title: Deficiency of the Lysosomal Protein CLN5 Alters Lysosomal Function and Movement.
CLN5 in heterozygosis may protect against the development of tumors in a VHL patient.
Title: CLN5 in heterozygosis may protect against the development of tumors in a VHL patient.
Association of the Recurrent Rare Variant c.415T>C p.Phe139Leu in CLN5 With a Recessively Inherited Macular Dystrophy.
Title: Association of the Recurrent Rare Variant c.415T>C p.Phe139Leu in CLN5 With a Recessively Inherited Macular Dystrophy.
Novel likely disease-causing CLN5 variants identified in Pakistani patients with neuronal ceroid lipofuscinosis.
Title: Novel likely disease-causing CLN5 variants identified in Pakistani patients with neuronal ceroid lipofuscinosis.
The Neuronal Ceroid Lipofuscinoses-Linked Loss of Function CLN5 and CLN8 Variants Disrupt Normal Lysosomal Function.
Title: The Neuronal Ceroid Lipofuscinoses-Linked Loss of Function CLN5 and CLN8 Variants Disrupt Normal Lysosomal Function.
This is the first report of whole gene deletion in combination with a novel pathogenic sequence variant in a CLN5 patient. The two mutations detected with whole exome sequencing simultaneously proved the advantage of the sequencing technology for genetic diagnostics
Title: A novel pathogenic frameshift variant unmasked by a large de novo deletion at 13q21.33-q31.1 in a Chinese patient with neuronal ceroid lipofuscinosis type 5.
This study demonstrated that Novel Mutations in CLN5 of Chinese Patients With Neuronal Ceroid Lipofuscinosis.
Title: Novel Mutations in CLN5 of Chinese Patients With Neuronal Ceroid Lipofuscinosis.

Submit: New GeneRIF Correction See all GeneRIFs (31)

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 5 MedGen: C1850442 OMIM: 256731 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH44829 (e-PCR)
- UniSTS:32625

STS-H96517 (e-PCR)
- UniSTS:14229

G32564 (e-PCR)
- UniSTS:117148

NoName (e-PCR)
- UniSTS:482008

SHGC-56376 (e-PCR)
- UniSTS:182749

RH46145 (e-PCR)
- UniSTS:48634

A009I22 (e-PCR)
- UniSTS:66813

CLN5 (e-PCR)
- UniSTS:505342

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables bis(monoacylglycero)phosphate synthase activity	IDA Inferred from Direct Assay more info	PubMed
enables hydrolase activity, acting on glycosyl bonds	IBA Inferred from Biological aspect of Ancestor more info
enables long-chain fatty acyl-CoA hydrolase activity	IDA Inferred from Direct Assay more info	PubMed
enables mannose binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	IEP Inferred from Expression Pattern more info	PubMed
involved_in glycosylation	IDA Inferred from Direct Assay more info	PubMed
involved_in lysosomal lumen acidification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lysosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in neurogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in neuron maturation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of GTP binding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein catabolic process	NAS Non-traceable Author Statement more info	PubMed
involved_in retrograde transport, endosome to Golgi	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in signal peptide processing	IDA Inferred from Direct Assay more info	PubMed
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in vacuolar lumen	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: bis(monoacylglycero)phosphate synthase CLN5

Names: BMP synthase CLN5; S-depalmitoylase CLN5; ceroid-lipofuscinosis neuronal protein 5; ceroid-lipofuscinosis, neuronal 5; palmitoyl protein thioesterase CLN5

NP_001353553.1

EC 3.1.2.22

NP_006484.2

EC 3.1.2.22

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_009064.1 RefSeqGene

Range

5001..15594

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_692

mRNA and Protein(s)

NM_001366624.2 → NP_001353553.1 bis(monoacylglycero)phosphate synthase CLN5 isoform 2

Status: REVIEWED

Source sequence(s)

AC001226

Consensus CDS

CCDS91815.1

UniProtKB/TrEMBL

A0A087WZY0, A0A1B0GTI0, A0A1B0GTR6

Related

ENSP00000489809.2, ENST00000636780.2

Conserved Domains (1) summary

pfam15014
Location:53 → 188

CLN5; Ceroid-lipofuscinosis neuronal protein 5
NM_006493.4 → NP_006484.2 bis(monoacylglycero)phosphate synthase CLN5 isoform 1

Status: REVIEWED

Source sequence(s)

AC001226

Consensus CDS

CCDS9456.2

UniProtKB/Swiss-Prot

B3KQK7, O75503

UniProtKB/TrEMBL

A0A1B0GWI2

Related

ENSP00000366673.5, ENST00000377453.9

Conserved Domains (1) summary

pfam15014
Location:53 → 349

CLN5; Ceroid-lipofuscinosis neuronal protein 5