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CLCN4 chloride voltage-gated channel 4 [ Homo sapiens (human) ]

Gene ID: 1183, updated on 27-Nov-2024

Summary

Official Symbol
CLCN4provided by HGNC
Official Full Name
chloride voltage-gated channel 4provided by HGNC
Primary source
HGNC:HGNC:2022
See related
Ensembl:ENSG00000073464 MIM:302910; AllianceGenome:HGNC:2022
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
CLC4; ClC-4; MRX15; MRX49; ClC-4A; MRXSRC
Summary
The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. Chloride channel 4 has an evolutionary conserved CpG island and is conserved in both mouse and hamster. This gene is mapped in close proximity to APXL (Apical protein Xenopus laevis-like) and OA1 (Ocular albinism type I), which are both located on the human X chromosome at band p22.3. The physiological role of chloride channel 4 remains unknown but may contribute to the pathogenesis of neuronal disorders. Alternate splicing results in two transcript variants that encode different proteins. [provided by RefSeq, Mar 2012]
Expression
Biased expression in brain (RPKM 20.8), heart (RPKM 5.1) and 10 other tissues See more
Orthologs
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Genomic context

See CLCN4 in Genome Data Viewer
Location:
Xp22.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (10156975..10237660)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (9739532..9820250)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (10125015..10205700)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9981409-9982292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9982293-9983176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20655 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:10008750-10009284 Neighboring gene claudin 34 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:10009285-10009817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:10014897-10015530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:10015531-10016163 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:10018119-10018742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:10050926-10051426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:10077459-10078176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:10078177-10078894 Neighboring gene WWC family member 3 Neighboring gene Sharpr-MPRA regulatory region 7563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:10141885-10142861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20656 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:10416979-10418178 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:10476778-10477647 Neighboring gene midline 1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:10539598-10539816 Neighboring gene MID1 promoter D Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:10579147-10580022 Neighboring gene RNA, U6 small nuclear 800, pseudogene Neighboring gene uncharacterized LOC124905245

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Intellectual disability, X-linked 49 Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2022-07-27)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2022-07-27)

ClinGen Genome Curation PagePubMed

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC163150

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables antiporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables antiporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables antiporter activity TAS
Traceable Author Statement
more info
 
enables chloride channel activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables voltage-gated chloride channel activity IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
involved_in chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chloride transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in chloride transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in monoatomic ion transmembrane transport TAS
Traceable Author Statement
more info
 
involved_in non-motile cilium assembly IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in ciliary base IEA
Inferred from Electronic Annotation
more info
 
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in early endosome membrane IEA
Inferred from Electronic Annotation
more info
 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in endosome membrane TAS
Traceable Author Statement
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in late endosome membrane IEA
Inferred from Electronic Annotation
more info
 
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in recycling endosome membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in synaptic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
H(+)/Cl(-) exchange transporter 4
Names
chloride channel 4
chloride channel protein 4
chloride channel, voltage-sensitive 4
chloride transporter ClC-4

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

  1. NG_012496.1 RefSeqGene

    Range
    5031..85716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256944.2NP_001243873.1  H(+)/Cl(-) exchange transporter 4 isoform 2

    See identical proteins and their annotated locations for NP_001243873.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC003666, AK299611, BP310547
    Consensus CDS
    CCDS59159.1
    UniProtKB/TrEMBL
    Q4G0X3
    Related
    ENSP00000501922.1, ENST00000674669.1
    Conserved Domains (2) summary
    cd03684
    Location:42490
    ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
    cd04591
    Location:513651
    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 ...
  2. NM_001830.4NP_001821.2  H(+)/Cl(-) exchange transporter 4 isoform 1

    See identical proteins and their annotated locations for NP_001821.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB019432, AC003666, BP310547
    Consensus CDS
    CCDS14137.1
    UniProtKB/Swiss-Prot
    A1L3U1, B7Z5Z4, P51793, Q9UBU1
    UniProtKB/TrEMBL
    Q4G0X3
    Related
    ENSP00000370213.4, ENST00000380833.9
    Conserved Domains (2) summary
    cd03684
    Location:78584
    ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
    cd04591
    Location:595745
    CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria

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

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    10156975..10237660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    9739532..9820250
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)