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

Summary

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: mouse all
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Genomic context

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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
functional interaction between ICln and HSPC038
Title: The molecular and functional interaction between ICln and HSPC038 proteins modulates the regulation of cell volume.
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.
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.
ICln interacts with integrin alphaIIbbeta3 and regulates platelet activation.
Title: ICln, a novel integrin alphaIIbbeta3-associated protein, functionally regulates platelet activation.
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.
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.
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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-22335 (e-PCR)
- UniSTS:15446

WI-20222 (e-PCR)
- UniSTS:50355

A006P03 (e-PCR)
- UniSTS:17613

RH12124 (e-PCR)
- UniSTS:53978

SHGC-31540 (e-PCR)
- UniSTS:58076

RH15619 (e-PCR)
- UniSTS:37859

SHGC-3577 (e-PCR)
- UniSTS:87278

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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)

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
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
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
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
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