Clcn6 chloride channel, voltage-sensitive 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clcn6provided by MGI
Official Full Name: chloride channel, voltage-sensitive 6provided by MGI
Primary source: MGI:MGI:1347049
See related: Ensembl:ENSMUSG00000029016 AllianceGenome:MGI:1347049
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Clc6
Summary: This gene encodes a member of the ClC chloride channel and transporter family of proteins. The encoded protein may function as a vesicular Cl-/H+ antiporter. Homozygous knockout mice exhibit decreased pain sensitivity, behavioral abnormalities and features of lysosomal storage disease. [provided by RefSeq, Aug 2015]
Expression: Ubiquitous expression in whole brain E14.5 (RPKM 17.3), CNS E14 (RPKM 16.1) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 E1; 4 78.67 cM

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (148088716..148123270, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (148004259..148038813, complement)

Chromosome 4 - NC_000070.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A Recurrent Gain-of-Function Mutation in CLCN6, Encoding the ClC-6 Cl(-)/H(+)-Exchanger, Causes Early-Onset Neurodegeneration.
Title: A Recurrent Gain-of-Function Mutation in CLCN6, Encoding the ClC-6 Cl(-)/H(+)-Exchanger, Causes Early-Onset Neurodegeneration.
This study demonistrated that clcn6 gene expression in mouse dorsal raphe nucleus
Title: Patterned expression of ion channel genes in mouse dorsal raphe nucleus determined with the Allen Mouse Brain Atlas.
Chloride channel 6 (Clcn6) deficient mice have a later-onset form of mild neurologic dysfunction similar to neuronal ceroid lipofuscinosis.
Title: Distinct neuropathologic phenotypes after disrupting the chloride transport proteins ClC-6 or ClC-7/Ostm1.
ClC-6 protein is almost exclusively expressed in neurons of the central and peripheral nervous systems, with a particularly high expression in dorsal root ganglia.
Title: Lysosomal storage disease upon disruption of the neuronal chloride transport protein ClC-6.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Gene trapped (1)
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables antiporter activity	IEA Inferred from Electronic Annotation more info
enables chloride transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables voltage-gated chloride channel activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in chloride transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in response to mechanical stimulus	ISO Inferred from Sequence Orthology more info
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in endosome	IEA Inferred from Electronic Annotation more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: H(+)/Cl(-) exchange transporter 6

Names: chloride channel 6; chloride channel protein 6; chloride transport protein 6; clC-6

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.

mRNA and Protein(s)

NM_011929.3 → NP_036059.1 H(+)/Cl(-) exchange transporter 6

See identical proteins and their annotated locations for NP_036059.1

Status: REVIEWED

Source sequence(s)

AK165362, AL606929, BM949055, BQ174789, BQ178271, CB521277, CX205353, CX564347

Consensus CDS

CCDS18928.1

UniProtKB/Swiss-Prot

O35454

UniProtKB/TrEMBL

A2A7F6, Q3UM91

Related

ENSMUSP00000030879.6, ENSMUST00000030879.12

Conserved Domains (5) summary

smart00116
Location:609 → 656

CBS; Domain in cystathionine beta-synthase and other proteins

COG0517
Location:804 → 854

CBS; CBS domain [Signal transduction mechanisms]

cd03685
Location:49 → 589

ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...

cd04591
Location:801 → 854

CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...

pfam00654
Location:140 → 571

Voltage_CLC; Voltage gated chloride channel