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Clcn4 Gene Detail
Summary
  • Symbol
    Clcn4
  • Name
    chloride channel, voltage-sensitive 4
  • Synonyms
    Clc4-2, Clcn4-2
  • Feature Type
    protein coding gene
  • IDs
    MGI:104571
    NCBI Gene: 12727
  • Alliance
    genome feature page
  • Transcription Start Sites
    5 TSS
Location &
Maps
more
  • Sequence Map
    Chr7:7285308-7303837 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 7, 4.23 cM, cytoband A2
  • Mapping Data
    6 experiments
Strain
Comparison
more
  • SNPs within 2kb
    638 from dbSNP Build 142
  • Strain Annotations
    15
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_104571
 protein coding gene Chr7:7285308-7303850 (-)
129S1/SvImJ ENSMUSG00200039961
 protein coding gene Chr7:4133033-4149850 (+)
A/J no annotation
AKR/J ENSMUSG00220021871
 protein coding gene Chr7:1641184-1658552 (-)
BALB/cJ ENSMUSG00180047287
 protein coding gene Chr7:3938102-3954328 (-)
C3H/HeJ ENSMUSG00175037514
 protein coding gene Chr7:5072009-5089235 (+)
C57BL/6NJ no annotation
CAROLI/EiJ MGP_CAROLIEiJ_G0029176
 protein coding gene Chr7:3924758-3980331 (-)
CAST/EiJ ENSTCUG00005022338
 protein coding gene Chr7:4161916-4178719 (-)
CBA/J no annotation
DBA/2J ENSMUSG00185043588
 protein coding gene Chr7:4158247-4175473 (-)
FVB/NJ ENSMUSG00205028813
 protein coding gene Chr7:3755038-3772366 (-)
JF1/MsJ ENSUMUG00000036327
 protein coding gene Chr7:4227669-4244565 (-)
LP/J ENSMUSG00230038619
 protein coding gene Chr7:7135654-7154525 (-)
NOD/ShiLtJ ENSMUSG00190038601
 protein coding gene Chr7:4015657-4032478 (-)
NZO/HlLtJ ENSMUSG00225019336
 protein coding gene Chr7:4979251-4998126 (-)
PWK/PhJ ENSLUMG00010039888
 protein coding gene Chr7:7695196-7712396 (-)
SPRET/EiJ ENSMSPG00010025005
 protein coding gene ChrX:150043625-150111196 (-)
WSB/EiJ no annotation



Homology
more
  • Human Ortholog
    CLCN4, Cl-/H+ antiporter 4
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CLCN4, Cl-/H+ antiporter 4
  • Synonyms
    ClC-4, CLC4, ClC-4A, MRX15, MRX49, MRXSRC
  • Links
    NCBI Gene ID: 1183
    UniProt: P51793

  • Chr Location
    Xp22.2; chrX:10156943-10237660 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with human CLCN4 associations

Human Disease Mouse Models
      
IDs
Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    1 phenotype from 1 allele in 1 genetic background
    2 phenotypes from multigenic genotypes
    6 phenotype references
Mice homozygous for a knock-out allele exhibit no obvious phenotype.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    36
  • GO References
    7
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    610
  • Tissues
    13
  • cDNA Data
    13
  • Literature Summary
    6
Sequences &
Gene Models
less
Representative SequencesLengthStrain/SpeciesFlank
genomic 12727 NCBI Gene Model | MGI Sequence Detail 18530 C57BL/6J ±  kb
transcript NR_178086 RefSeq | MGI Sequence Detail 5263 ZRU/MplStud  
polypeptide Q61418 UniProt | EBI | MGI Sequence Detail 747 Not Applicable  
For the selected sequence
Protein
Information
less
Molecular
Reagents
less
  • All nucleic 25
    cDNA 22
    Primer pair 3

    Microarray probesets 5
Other
Accession IDs
less
MGD-MRK-26005
References
more
  • Summaries
    All 44
    Developmental Gene Expression 6
    Gene Ontology 7
    Phenotypes 6
  • Earliest
    J:26310 Rugarli EI, et al., Different chromosomal localization of the Clcn4 gene in Mus spretus and C57BL/6J mice [see comments]. Nat Genet. 1995 Aug;10(4):466-71
  • Latest
    J:370066 Lee SM, et al., Developmental deficits, synapse and dendritic abnormalities in a Clcn4 KO autism mice model: endophenotypic target for ASD. Transl Psychiatry. 2025 Jan 25;15(1):28
Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources
Funding Information
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Send questions and comments to User Support. 		last database update
09/01/2026
MGI 6.24 		The Jackson Laboratory