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CLNS1A chloride nucleotide-sensitive channel 1A [ Homo sapiens (human) ]

Gene ID: 1207, updated on 5-Mar-2024

Summary

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Official Symbol
CLNS1Aprovided by HGNC
Official Full Name
chloride nucleotide-sensitive channel 1Aprovided by HGNC
Primary source
HGNC:HGNC:2080
See related
Ensembl:ENSG00000074201 MIM:602158; AllianceGenome:HGNC:2080
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
CLCI; ICln; CLNS1B
Summary
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]
Expression
Ubiquitous expression in adrenal (RPKM 36.6), brain (RPKM 32.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11q14.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (77614530..77637794, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (77547583..77570850, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (77325575..77348839, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak1361 silencer Neighboring gene long intergenic non-protein coding RNA 3030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3800 Neighboring gene MPRA-validated peak1362 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr11:77316282-77316821 Neighboring gene aquaporin 11 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:77348567-77349086 Neighboring gene uncharacterized LOC107984369 Neighboring gene CRISPRi-validated cis-regulatory element chr11.4537 Neighboring gene MPRA-validated peak1363 silencer Neighboring gene remodeling and spacing factor 1 Neighboring gene ferritin heavy chain 1 pseudogene 16

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. The ICln interactome. Fürst J, et al. Acta Physiol (Oxf), 2006 May-Jun. PMID 16734741
  2. Volume-regulated Cl- channels in human pleural mesothelioma cells. Meyer G, et al. FEBS Lett, 2004 Feb 13. PMID 14960305
  3. Modulation of volume regulated anion current by I(Cln). Hubert MD, et al. Biochim Biophys Acta, 2000 Jun 1. PMID 10825435
  4. pICln inhibits snRNP biogenesis by binding core spliceosomal proteins. Pu WT, et al. Mol Cell Biol, 1999 Jun. PMID 10330151, Free PMC Article
  5. The ubiquitously expressed pICln protein forms homomeric complexes in vitro. Buyse G, et al. Biochem Biophys Res Commun, 1996 Jan 26. PMID 8579598

See all (121) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. O-GlcNAcylated LARP1 positively regulated by circCLNS1A facilitates hepatoblastoma progression through DKK4/beta-catenin signalling.
    Title: O-GlcNAcylated LARP1 positively regulated by circCLNS1A facilitates hepatoblastoma progression through DKK4/β-catenin signalling.
  2. Protein Arginine Methyltransferase 5 Promotes pICln-Dependent Androgen Receptor Transcription in Castration-Resistant Prostate Cancer.
    Title: Protein Arginine Methyltransferase 5 Promotes pICln-Dependent Androgen Receptor Transcription in Castration-Resistant Prostate Cancer.
  3. the S. pombe ICln protein is required for optimal production of the spliceosomal snRNPs and for efficient splicing in vivo
    Title: Characterization and in vivo functional analysis of the Schizosaccharomyces pombe ICLN gene.
  4. functional interaction between ICln and HSPC038
    Title: The molecular and functional interaction between ICln and HSPC038 proteins modulates the regulation of cell volume.
  5. RioK1, a new interactor of protein arginine methyltransferase 5 (PRMT5), competes with pICln for binding and modulates PRMT5 complex composition and substrate specificity.
    Title: RioK1, a new interactor of protein arginine methyltransferase 5 (PRMT5), competes with pICln for binding and modulates PRMT5 complex composition and substrate specificity.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. ICln interacts with integrin alphaIIbbeta3 and regulates platelet activation.
    Title: ICln, a novel integrin alphaIIbbeta3-associated protein, functionally regulates platelet activation.
  8. revealed an increase of ICln in the mesothelioma cell membrane under hypotonic conditions, an event possibly related to the activation of Cl(-) channels
    Title: Volume-regulated Cl- channels in human pleural mesothelioma cells.
  9. Data show that ICln159, a truncated ICln mutant, belongs to the pleckstrin homology (PH) domain family of proteins and interacts with LSm4, a protein involved in splicing and mRNA degradation.
    Title: ICln159 folds into a pleckstrin homology domain-like structure. Interaction with kinases and the splicing factor LSm4.
  10. Lsm10 and Lsm11, which replace the Sm proteins D1 and D2 in the histone RNA processing U7 snRNPs, associate with pICln in vitro and in vivo without receiving sDMA modifications and with PRMT5 and SMN complexes
    Title: Toward an assembly line for U7 snRNPs: interactions of U7-specific Lsm proteins with PRMT5 and SMN complexes.
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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of chloride channel, nucleotide-sensitive, 1A (CLNS1A) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell volume homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in chloride transport IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA cis splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in spliceosomal snRNP assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spliceosomal snRNP assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spliceosomal snRNP assembly NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of methylosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of pICln-Sm protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of pICln-Sm protein complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
part_of spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
methylosome subunit pICln
Names
chloride channel regulatory protein
chloride channel, nucleotide sensitive 1A
chloride conductance regulatory protein ICln
chloride ion current inducer protein
i(Cln)
reticulocyte pICln
reticulocyte protein ICln

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.

mRNA and Protein(s)

  1. NM_001293.3 → NP_001284.1  methylosome subunit pICln isoform a

    See identical proteins and their annotated locations for NP_001284.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AA757599, AF005422, AP000609, DA004269
    Consensus CDS
    CCDS8252.1
    UniProtKB/Swiss-Prot
    B2RCS9, P54105, Q0VDK6, Q9NRD2, Q9NRD3
    Related
    ENSP00000433919.1, ENST00000525428.6
    Conserved Domains (1) summary
    pfam03517
    Location:35 → 137
    Voldacs; Regulator of volume decrease after cellular swelling

  2. NM_001311199.2 → NP_001298128.1  methylosome subunit pICln isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AP000609, BQ643786, DA004269
    Consensus CDS
    CCDS8252.1
    UniProtKB/Swiss-Prot
    B2RCS9, P54105, Q0VDK6, Q9NRD2, Q9NRD3
    Related
    ENSP00000434311.1, ENST00000528364.1
    Conserved Domains (1) summary
    pfam03517
    Location:35 → 137
    Voldacs; Regulator of volume decrease after cellular swelling

  3. NM_001311200.2 → NP_001298129.1  methylosome subunit pICln isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AA757599, AL530926, AP000609, DA004269, U53454
    Consensus CDS
    CCDS81601.1
    UniProtKB/TrEMBL
    J3KN38
    Related
    ENSP00000263309.3, ENST00000263309.7
    Conserved Domains (1) summary
    pfam03517
    Location:35 → 103
    Voldacs; Regulator of volume decrease after cellular swelling

  4. NM_001311201.2 → NP_001298130.1  methylosome subunit pICln isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AA757599, AP000609, BU538016, DA004269, U53454
    Consensus CDS
    CCDS81602.1
    UniProtKB/TrEMBL
    E9PJF4
    Related
    ENSP00000433741.1, ENST00000525064.5
    Conserved Domains (1) summary
    pfam03517
    Location:35 → 137
    Voldacs; Regulator of volume decrease after cellular swelling

  5. NM_001311202.2 → NP_001298131.1  methylosome subunit pICln isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AA757599, AP000609, BU169662, U53454
    Consensus CDS
    CCDS81600.1
    UniProtKB/TrEMBL
    E9PMI6
    Related
    ENSP00000434963.1, ENST00000532069.5
    Conserved Domains (1) summary
    cl17171
    Location:35 → 84
    PH-like; Pleckstrin homology-like domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    77614530..77637794 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    77547583..77570850 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P54105.1 GenPept UniProtKB/Swiss-Prot:P54105

Gene LinkOut

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