This gene encodes a protein that functions in multiple regulatory pathways. The encoded protein complexes with numerous cytosolic proteins and performs diverse functions including regulation of small nuclear ribonucleoprotein biosynthesis, platelet activation and cytoskeletal organization. The protein is also found associated with the plasma membrane where it functions as a chl... See more...

Aliases for CLNS1A Gene

Aliases for CLNS1A Gene

  • Chloride Nucleotide-Sensitive Channel 1A 2 3 5
  • Methylosome Subunit PICln 2 3 4
  • Chloride Conductance Regulatory Protein ICln 3 4
  • Chloride Channel, Nucleotide Sensitive 1A 3 4
  • Chloride Ion Current Inducer Protein 3 4
  • Reticulocyte PICln 3 4
  • I(Cln) 3 4
  • CLCI 3 4
  • Chloride Channel, Nucleotide-Sensitive, 1A 2
  • Chloride Channel Regulatory Protein 3
  • Reticulocyte Protein ICln 3
  • CLNS1B 3
  • ICln 3
  • ClCI 4
  • ICLN 4

External Ids for CLNS1A Gene

Previous HGNC Symbols for CLNS1A Gene

  • CLCI

Previous GeneCards Identifiers for CLNS1A Gene

  • GC11M079654
  • GC11M078866
  • GC11M077549
  • GC11M077053
  • GC11M077004
  • GC11M077327
  • GC11M073625
  • GC11M077225

Summaries for CLNS1A Gene

Entrez Gene Summary for CLNS1A Gene

  • This gene encodes a protein that functions in multiple regulatory pathways. The encoded protein complexes with numerous cytosolic proteins and performs diverse functions including regulation of small nuclear ribonucleoprotein biosynthesis, platelet activation and cytoskeletal organization. The protein is also found associated with the plasma membrane where it functions as a chloride current regulator. Pseudogenes of this gene are found on chromosomes 1, 4 and 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]

GeneCards Summary for CLNS1A Gene

CLNS1A (Chloride Nucleotide-Sensitive Channel 1A) is a Protein Coding gene. Among its related pathways are Neuropathic Pain-Signaling in Dorsal Horn Neurons and Transport of the SLBP independent Mature mRNA. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity.

UniProtKB/Swiss-Prot Summary for CLNS1A Gene

  • Involved in both the assembly of spliceosomal snRNPs and the methylation of Sm proteins (PubMed:21081503, PubMed:18984161). Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway.

Gene Wiki entry for CLNS1A Gene

Additional gene information for CLNS1A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLNS1A Gene

Genomics for CLNS1A Gene

GeneHancer (GH) Regulatory Elements for CLNS1A Gene

Promoters and enhancers for CLNS1A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J077636 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 513.1 +0.6 605 3.2 FOXK2 ZBTB40 ZNF217 SIN3A NRF1 TCF12 USF1 POLR2G SP1 GTF2E2 CLNS1A INTS4 AAMDC RSF1 lnc-CLNS1A-3
GH11J077588 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11.9 +47.4 47418 4 NRF1 POLR2G NCOR1 PHF8 ZFX ZNF10 ZIC2 POLR2A KDM6A ZBTB10 AQP11 AAMDC INTS4 CLNS1A GDPD4 lnc-CLNS1A-3
GH11J077630 Enhancer 0.9 ENCODE 12.8 +6.8 6841 1.6 NCOR1 SKI TEAD1 FOXA2 KMT2B BCL11A CBFB ZNF384 USF1 SAP130 CLNS1A INTS4 AQP11 lnc-CLNS1A-3
GH11J077601 Enhancer 0.9 Ensembl ENCODE 12.6 +35.1 35052 2.7 TCF12 JUND FOS EP300 ZNF316 MAFF POLR2A NR3C1 FOSL2 MAFK AAMDC CLNS1A MYO7A AQP11 lnc-CLNS1A-3
GH11J076652 Promoter/Enhancer 1.1 Ensembl ENCODE dbSUPER 4.7 +982.4 982399 5 FOS RBM25 REST ZFHX2 BCOR ADNP VEZF1 GLIS1 CEBPB ZMYM3 LOC107984360 ENSG00000254810 LINC02757 CLNS1A lnc-THAP12-4 LRRC32
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLNS1A on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLNS1A

Top Transcription factor binding sites by QIAGEN in the CLNS1A gene promoter:
  • Cart-1
  • E47
  • Hand1
  • NCX
  • POU2F1
  • POU2F1a
  • USF-1
  • USF-1:USF-2
  • USF1
  • USF2

Genomic Locations for CLNS1A Gene

Genomic Locations for CLNS1A Gene
chr11:77,514,936-77,637,806
(GRCh38/hg38)
Size:
122,871 bases
Orientation:
Minus strand
chr11:77,225,981-77,348,851
(GRCh37/hg19)
Size:
122,871 bases
Orientation:
Minus strand

Genomic View for CLNS1A Gene

Genes around CLNS1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLNS1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLNS1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLNS1A Gene

Proteins for CLNS1A Gene

  • Protein details for CLNS1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P54105-ICLN_HUMAN
    Recommended name:
    Methylosome subunit pICln
    Protein Accession:
    P54105
    Secondary Accessions:
    • B2RCS9
    • Q0VDK6
    • Q9NRD2
    • Q9NRD3

    Protein attributes for CLNS1A Gene

    Size:
    237 amino acids
    Molecular mass:
    26215 Da
    Quaternary structure:
    • Component of the methylosome, a 20S complex containing at least PRMT5/SKB1, WDR77/MEP50 and CLNS1A/pICln (PubMed:21081503, PubMed:11747828, PubMed:18984161). May mediate SNRPD1 and SNRPD3 methylation. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP (PubMed:18984161). Interacts with LSM10 and LSM11 (PubMed:16087681).

neXtProt entry for CLNS1A Gene

Post-translational modifications for CLNS1A Gene

  • Ubiquitination at Lys5 and Lys30
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CLNS1A Gene

Domains & Families for CLNS1A Gene

Gene Families for CLNS1A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transporters

Protein Domains for CLNS1A Gene

Blocks:
  • Nucleotide-sensitive chloride conductance regulator (ICln) signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLNS1A Gene

GenScript: Design optimal peptide antigens:
  • Reticulocyte pICln (ICLN_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P54105

UniProtKB/Swiss-Prot:

ICLN_HUMAN :
  • Belongs to the pICln (TC 1.A.47) family.
Family:
  • Belongs to the pICln (TC 1.A.47) family.
genes like me logo Genes that share domains with CLNS1A: view

Function for CLNS1A Gene

Molecular function for CLNS1A Gene

UniProtKB/Swiss-Prot Function:
Involved in both the assembly of spliceosomal snRNPs and the methylation of Sm proteins (PubMed:21081503, PubMed:18984161). Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway.
GENATLAS Biochemistry:
chloride channel nucleotide sensitive,swelling-dependent outwardly rectifying,ICLN type 1A,26kDa,nucleotide sensitive expressed in ocular ciliary epithelium,mouse Icln ortholog

Phenotypes From GWAS Catalog for CLNS1A Gene

Gene Ontology (GO) - Molecular Function for CLNS1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 11756452
GO:0046982 protein heterodimerization activity IDA 18495660
genes like me logo Genes that share ontologies with CLNS1A: view
genes like me logo Genes that share phenotypes with CLNS1A: view

Animal Models for CLNS1A Gene

MGI Knock Outs for CLNS1A:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLNS1A

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLNS1A Gene

Localization for CLNS1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLNS1A Gene

Cytoplasm, cytosol. Nucleus. Cytoplasm, cytoskeleton. Note=A small fraction is also associated with the cytoskeleton (PubMed:18984161).

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLNS1A gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 4
cytoskeleton 4
extracellular 2
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
  • Microtubules (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLNS1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005634 nucleus IEA,IDA 21081503
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with CLNS1A: view

Pathways & Interactions for CLNS1A Gene

PathCards logo

SuperPathways for CLNS1A Gene

SuperPathway Contained pathways
1 Activation of cAMP-Dependent PKA
.77
.77
.56
2 Transport of the SLBP independent Mature mRNA
3 RNA transport
4 Neuropathic Pain-Signaling in Dorsal Horn Neurons
.40
5 Hepatic ABC Transporters
.41
genes like me logo Genes that share pathways with CLNS1A: view

Pathways by source for CLNS1A Gene

3 Reactome pathways for CLNS1A Gene
1 KEGG pathway for CLNS1A Gene
5 Qiagen pathways for CLNS1A Gene
  • Activation of cAMP-Dependent PKA
  • cAMP Pathway
  • Cholera Infection
  • Hepatic ABC Transporters
  • PKA Signaling

Gene Ontology (GO) - Biological Process for CLNS1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000387 spliceosomal snRNP assembly TAS --
GO:0006821 chloride transport IEA --
GO:0006884 cell volume homeostasis IEA --
genes like me logo Genes that share ontologies with CLNS1A: view

No data available for SIGNOR curated interactions for CLNS1A Gene

Drugs & Compounds for CLNS1A Gene

(2) Drugs for CLNS1A Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Chloride ion Experimental Pharma 0

(2) Additional Compounds for CLNS1A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLNS1A: view

Transcripts for CLNS1A Gene

mRNA/cDNA for CLNS1A Gene

5 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLNS1A

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLNS1A Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c · 8d · 8e
SP1: -
SP2: - -
SP3: - -
SP4: - - - -
SP5: - -
SP6: - - - -
SP7:
SP8:
SP9: - - - -

Relevant External Links for CLNS1A Gene

GeneLoc Exon Structure for
CLNS1A

Expression for CLNS1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLNS1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLNS1A Gene

This gene is overexpressed in Lymph node (6.7) and Peripheral blood mononuclear cells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLNS1A Gene



Protein tissue co-expression partners for CLNS1A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLNS1A

SOURCE GeneReport for Unigene cluster for CLNS1A Gene:

Hs.430733

Evidence on tissue expression from TISSUES for CLNS1A Gene

  • Nervous system(4.6)
  • Kidney(4.5)
  • Eye(4.4)
  • Liver(4.4)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with CLNS1A: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLNS1A Gene

Orthologs for CLNS1A Gene

This gene was present in the common ancestor of animals.

Orthologs for CLNS1A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLNS1A 31 30
  • 99.86 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CLNS1A 31 30
  • 93.11 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 93 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
dog
(Canis familiaris)
Mammalia CLNS1A 31 30
  • 91.21 (n)
OneToMany
-- 31
  • 91 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Clns1a 17 31 30
  • 88.28 (n)
rat
(Rattus norvegicus)
Mammalia Clns1a 30
  • 88.28 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLNS1A 31
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLNS1A 31 30
  • 75.32 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLNS1A 31
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clns1a 30
  • 71.49 (n)
Str.2882 30
African clawed frog
(Xenopus laevis)
Amphibia ICLN 30
zebrafish
(Danio rerio)
Actinopterygii icln 31 30 30
  • 67.09 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1213 30
fruit fly
(Drosophila melanogaster)
Insecta icln 31
  • 30 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea icln-1 31
  • 29 (a)
OneToOne
Species where no ortholog for CLNS1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CLNS1A Gene

ENSEMBL:
Gene Tree for CLNS1A (if available)
TreeFam:
Gene Tree for CLNS1A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLNS1A: view image

Paralogs for CLNS1A Gene

Pseudogenes.org Pseudogenes for CLNS1A Gene

genes like me logo Genes that share paralogs with CLNS1A: view

No data available for Paralogs for CLNS1A Gene

Variants for CLNS1A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLNS1A Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
VAR_015736 - p.Gln20His
VAR_015737 - p.Met218Thr

Additional dbSNP identifiers (rs#s) for CLNS1A Gene

Structural Variations from Database of Genomic Variants (DGV) for CLNS1A Gene

Variant ID Type Subtype PubMed ID
dgv1234n100 CNV gain 25217958
esv3626888 CNV loss 21293372
nsv468641 CNV gain 19166990
nsv555452 CNV gain 21841781

Variation tolerance for CLNS1A Gene

Residual Variation Intolerance Score: 51.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.64; 13.79% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLNS1A Gene

Human Gene Mutation Database (HGMD)
CLNS1A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLNS1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLNS1A Gene

Disorders for CLNS1A Gene

Additional Disease Information for CLNS1A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CLNS1A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLNS1A Gene

Publications for CLNS1A Gene

  1. Modulation of volume regulated anion current by I(Cln). (PMID: 10825435) Hubert MD … Garber SS (Biochimica et biophysica acta 2000) 3 4 23 54
  2. Chromosomal localization of the genes (CLNS1A and CLNS1B) coding for the swelling-dependent chloride channel ICln. (PMID: 8975725) Nagl UO … Paulmichl M (Genomics 1996) 2 3 23 54
  3. The ubiquitously expressed pICln protein forms homomeric complexes in vitro. (PMID: 8579598) Buyse G … Eggermont J (Biochemical and biophysical research communications 1996) 3 4 23 54
  4. Molecular cloning of the human volume-sensitive chloride conductance regulatory protein, pICln, from ocular ciliary epithelium. (PMID: 7887970) Anguita J … Coca-Prados M (Biochemical and biophysical research communications 1995) 2 3 4 54
  5. RioK1, a new interactor of protein arginine methyltransferase 5 (PRMT5), competes with pICln for binding and modulates PRMT5 complex composition and substrate specificity. (PMID: 21081503) Guderian G … Grimmler M (The Journal of biological chemistry 2011) 3 4 54

Products for CLNS1A Gene

Sources for CLNS1A Gene