CLCNKA protein expression summary - The Human Protein Atlas

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CLCNKA

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HUMAN PROTEIN ATLAS SUMMARYⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Proteinⁱ Full gene name according to HGNC.	Chloride voltage-gated channel Ka
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	CLCNKA (hClC-Ka)
Tissue specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Group enriched (kidney, parathyroid gland)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enriched (Late spermatids)
Blood specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed blood cell samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Not detected in immune cells
Brain specificityⁱ The regional specificity category is based on mRNA expression levels in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression profile is based on a combination of data from GTEX and FANTOM5. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Human brain regional enriched (cerebellum)
Cancer prognostic summary	Gene product is not prognostic
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Membrane
Protein function (UniProt)ⁱ Useful information about the protein provided by UniProt.	Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport. May be important in urinary concentrating mechanisms.... show less
Molecular function (UniProt)ⁱ Keywords assigned by UniProt to proteins due to their particular molecular function.	Chloride channel, Ion channel, Voltage-gated channel
Biological process (UniProt)ⁱ Keywords assigned by UniProt to proteins because they are involved in a particular biological process.	Ion transport, Transport
Disease involvementⁱ Disease related keywords assigned by UniProt combined with Cancer-related genes and FDA approved drug targets Read more	Bartter syndrome, Deafness, Disease mutation
Ligand (UniProt)ⁱ Keywords assigned by UniProt to proteins because they bind, are associated with, or whose activity is dependent of some molecule.	Calcium, Chloride, Metal-binding
Gene summary (Entrez)ⁱ Useful information about the gene from Entrez	This gene is a member of the CLC family of voltage-gated chloride channels. The encoded protein is predicted to have 12 transmembrane domains, and requires a beta subunit called barttin to form a functional channel. It is thought to function in salt reabsorption in the kidney and potassium recycling in the inner ear. The gene is highly similar to CLCNKB, which is located 10 kb downstream from this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]... show less

TISSUE ATLASⁱ Summary of data presented in the Tissue Atlas and representative images of protein expression (left) and mRNA expression (right). The images are clickable and will redirect to more Tissue Atlas data. The Tissue Atlas contains information regarding the expression profiles of protein-coding genes in normal human tissue, both on the mRNA and protein level. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more

Tissue specificity (RNA)ⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Group enriched (kidney, parathyroid gland)
Tissue distribution (RNA)ⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in some
Protein expressionⁱ A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation. "Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile. Read more	Cytoplasmic expression in kidney, salivary and thyroid glands.

SINGLE CELL TYPE ATLASⁱ Summary of data presented in the Cell Type Atlas and an interactive image showing mRNA expression in cell type groups e.g. epithelial cells and germ cells. The image is clickable and will redirect to more Cell Type Atlas data. The Cell Type Atlas contains information about single cell type RNA expression based on scRNAseq of human tissues. The data also covers transcriptomics analysis of human blood and cultured cell lines. Read more

Cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enriched (Late spermatids)
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines.	Cell line enriched (U-266/70)

PATHOLOGY ATLASⁱ Summary of data presented in the Pathology Atlas , with representative images of protein expression in cancer (left) and correlation between mRNA expression and patient survival (right). Images are clickable and redirect to pages with more Pathology Atlas data. The Pathology Atlas contains mRNA and protein expression data from 17 different forms of human cancer, as well as correlation analysis of mRNA expression and patient survival. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more

Prognostic summary	Gene product is not prognostic
Cancer specificity (RNA)ⁱ Specificity of RNA expression in 17 cancer types is categorized as either cancer enriched, group enriched, cancer enhanced, low cancer specificity and not detected. Read more	Group enriched (renal cancer, thyroid cancer)
Cancer distribution (RNA)ⁱ Distribution of RNA expression in 17 cancer types is categorized as either detected in single, detected in some, detected in many, detected in all, or not detected. Read more	Detected in some

Human regional specificityⁱ

Region enriched (cerebellum)

BLOOD ATLASⁱ Summary of data presented in the Blood Atlas and a representative image of mRNA expression in immune cells in the blood. The image is clickable and will redirect to more Blood Atlas data. The Blood Atlas contains single cell type RNA information covering various immune cells in the blood, e.g. B-cells and granulocytes. Analysis of the human secretome (including annotation of the genes predicted to be actively secreted to human blood) and proteins detected in human blood are also presented. Read more

Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Not detected
Detected in blood by immunoassayⁱ The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search. Read more	No (not applicable)
Detected in blood by mass spectrometryⁱ Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.	No

CELL ATLASⁱ Summary of data presented in the Cell Atlas and a representative image of subcellular localization. The Cell Atlas provides RNA expression data derived from RNA sequencing of a large panel of cell lines and protein localization data derived from antibody-based profiling by immunofluorescence confocal microscopy, using a subset of cell lines selected based on RNA expression. Read more

Main locationⁱ Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or ihigher staining intensity compared to the potential additional location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively. Read more	Not available
Cell cycle dependencyⁱ Cell-cycle dependance of single-cell varations in RNA and/or protein expression as observed in an additional assay for characterizing single-cell varations. "NA" indicates a lack of such data. Read more	NA

GENE INFORMATIONⁱ Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name	CLCNKA (HGNC Symbol)
Synonyms	hClC-Ka
Description	Chloride voltage-gated channel Ka (HGNC Symbol)
Chromosome	1
Cytoband	p36.13
Chromosome location (bp)	16018875 - 16034050
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3
Protein evidence	Evidence at protein level (all genes)
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes
Ensembl	ENSG00000186510 (version 92.38)
Entrez gene	1187
UniProt	P51800 (UniProt - Evidence at protein level)
neXtProt	NX_P51800
Antibodypedia	CLCNKA antibodies

PROTEIN BROWSERⁱ

CLCNKA-201

CLCNKA-202

CLCNKA-203

PROTEIN INFORMATIONⁱ The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database. The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein. The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class. The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Splice variant	UniProt	Protein class	Gene ontology	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
CLCNKA-201 ENSP00000332771 ENST00000331433	P51800 [Direct mapping] Chloride channel protein ClC-Ka Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based >9TM proteins predicted by MDM Disease related genes Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0005244 [voltage-gated ion channel activity] GO:0005247 [voltage-gated chloride channel activity] GO:0005254 [chloride channel activity] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0006811 [ion transport] GO:0006821 [chloride transport] GO:0007588 [excretion] GO:0016020 [membrane] GO:0016021 [integral component of membrane] GO:0034220 [ion transmembrane transport] GO:0034707 [chloride channel complex] GO:0034765 [regulation of ion transmembrane transport] GO:0042802 [identical protein binding] GO:0046872 [metal ion binding] GO:0055085 [transmembrane transport] GO:1902476 [chloride transmembrane transport] Show all	687 aa 75.3 kDa	No	>9
CLCNKA-202 ENSP00000364844 ENST00000375692	P51800 [Direct mapping] Chloride channel protein ClC-Ka Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based >9TM proteins predicted by MDM Disease related genes Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0005244 [voltage-gated ion channel activity] GO:0005247 [voltage-gated chloride channel activity] GO:0005254 [chloride channel activity] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0006811 [ion transport] GO:0006821 [chloride transport] GO:0007588 [excretion] GO:0016020 [membrane] GO:0016021 [integral component of membrane] GO:0034220 [ion transmembrane transport] GO:0034707 [chloride channel complex] GO:0034765 [regulation of ion transmembrane transport] GO:0042802 [identical protein binding] GO:0046872 [metal ion binding] GO:0055085 [transmembrane transport] GO:1902476 [chloride transmembrane transport] Show all	686 aa 75.2 kDa	No	>9
CLCNKA-203 ENSP00000414445 ENST00000439316	P51800 [Direct mapping] Chloride channel protein ClC-Ka Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based >9TM proteins predicted by MDM Disease related genes Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0005244 [voltage-gated ion channel activity] GO:0005247 [voltage-gated chloride channel activity] GO:0005254 [chloride channel activity] GO:0005886 [plasma membrane] GO:0005887 [integral component of plasma membrane] GO:0006811 [ion transport] GO:0006821 [chloride transport] GO:0007588 [excretion] GO:0016020 [membrane] GO:0016021 [integral component of membrane] GO:0034220 [ion transmembrane transport] GO:0034707 [chloride channel complex] GO:0034765 [regulation of ion transmembrane transport] GO:0042802 [identical protein binding] GO:0046872 [metal ion binding] GO:0055085 [transmembrane transport] GO:1902476 [chloride transmembrane transport] Show all	644 aa 70.5 kDa	No	>9

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The Human Protein Atlas project is funded
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