CLCN6
Chloride Voltage-Gated Channel 6
Gene Information Card
| Symbol | CLCN6 |
|---|---|
| Full Name | Chloride Voltage-Gated Channel 6 |
| Gene Type | Protein coding |
| Chromosomal Location | 1p36.21 |
| NCBI Gene ID | 1185 ncbi.nlm.nih.gov/gene/1185 |
| Ensembl ID | ENSG00000111011 |
| UniProt ID | P51797 |
| OMIM ID | 602726 |
| HGNC ID | 2026 |
| Aliases | CIC-6, ClC-6a, ClC-6b |
Description
CLCN6 encodes a member of the voltage-gated chloride channel (CLC) family. The protein functions as a chloride/proton antiporter localized to endosomes and lysosomes, playing a role in intracellular ion homeostasis and vesicular acidification. Mutations in CLCN6 are associated with neurodegenerative disorders.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Neuronal ceroid lipofuscinosis (CLN6 disease) | Loss-of-function mutations impair lysosomal chloride transport, leading to accumulation of autofluorescent lipopigments in neurons. | ClinVar, OMIM |
| Epilepsy, progressive myoclonic | Missense variants disrupt channel function, causing neuronal hyperexcitability. | ClinVar, OMIM |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Testis | 8.3 | Low |
| Kidney | 6.1 | Low |
| Lung | 4.7 | Low |
| Liver | 3.2 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| SH-SY5Y | 15.2 | Neuroblastoma cell line |
| HEK 293 | 9.8 | Embryonic kidney cells |
| HeLa | 7.4 | Cervical carcinoma cells |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.316C>T (p.Arg106Cys) | Missense | <0.01% | Reduced chloride transport activity |
| c.535G>A (p.Gly179Arg) | Missense | <0.01% | Impaired protein trafficking to lysosomes |
| c.1000C>T (p.Arg334Trp) | Missense | <0.01% | Loss of antiporter function |
Mutation functional classification
Loss of Function (LOF)
Most pathogenic mutations reduce or abolish chloride/proton exchange, leading to lysosomal dysfunction.
Gain of Function (GOF)
Not reported.
Dominant Negative (DN)
Not reported.
View complete mutation data：
Gene Ontology (GO)
| • voltage-gated chloride channel activity | • chloride transmembrane transport |
| • endosome | • lysosome |
| • intracellular pH regulation |
Pathways
• Lysosomal acidification
• Ion transport by P-type ATPases
Protein Summary
The CLCN6 protein (ClC-6) is a 869-amino acid transmembrane protein that functions as a 2Cl-/1H+ antiporter. It is predominantly expressed in the brain and localizes to late endosomes and lysosomes, where it contributes to luminal acidification and chloride homeostasis. Defects in ClC-6 cause lysosomal storage disease.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| CLCN6 Knockout HEK293 Cell Line | EDJ-KQ2569 | Human | 1185 | Details Get a Quote |
| CLCN6 Knockout HeLa Cell Line | EDJ-KQ18187 | Human | 1185 | Details Get a Quote |
| CLCN6 Knockout A-549 Cell Line | EDJ-KQ23246 | Human | 1185 | Details Get a Quote |
| CLCN6 Knockout HCT 116 Cell Line | EDJ-KQ23247 | Human | 1185 | Details Get a Quote |
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