HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CLNS1A
chloride nucleotide-sensitive channel 1A
Chromosome 11 · 11q14.1
NCBI Gene: 1207Ensembl: ENSG00000074201.10HGNC: HGNC:2080UniProt: E9PJF4
134PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
RNA bindingprotein bindingspliceosomal snRNP assemblycytosolAlzheimer diseaseParkinson diseaselysosomal storage diseasemultiple sclerosis
✦AI Summary

CLNS1A (chloride nucleotide-sensitive channel 1A) is a multifunctional protein serving dual roles in spliceosomal assembly and methylosome function. Primarily, CLNS1A acts as a chaperone regulating assembly of spliceosomal U1, U2, U4, and U5 snRNPs by sequestering Sm proteins in an inactive 6S pICln-Sm complex in the cytosol until the SMN complex triggers their transfer to form core snRNPs 12. Beyond splicing, CLNS1A interacts with protein arginine methyltransferase 5 (PRMT5) as an adaptor protein enabling substrate recruitment to the methylosome complex 3. This PRMT5-CLNS1A axis regulates symmetric histone and Sm protein dimethylation, critical for proper spliceosome function and mRNA chr11 escape 4. Disease relevance spans both immunology and oncology. CLNS1A deletion in CD4 T cells impairs proliferation and effector function by disrupting genome stability and cell cycle progression, protecting mice from experimental autoimmune encephalomyelitis and inflammatory bowel disease 5. In non-small cell lung cancer, CLNS1A overexpression correlates with poor survival and promotes chemoresistance through both chloride channel-dependent drug efflux and FAK-SRC-RAC1 pathway activation 6. CLNS1A depletion impairs detained intron splicing regulation, representing a therapeutic vulnerability in cancer cells dependent on proper PRMT5-mediated splicing 7. These findings establish CLNS1A as both a fundamental RNA processing factor and emerging therapeutic target.

Sources cited
1
CLNS1A functions as a chaperone regulating spliceosomal snRNP assembly and Sm protein complex formation
PMID: 10330151
2
CLNS1A controls assembly of core snRNPs and their nuclear transport through interaction with SMN complex
PMID: 18984161
3
CLNS1A is a substrate adaptor for PRMT5 with a conserved peptide sequence required for methylosome function
PMID: 34358446
4
CLNS1A deletion in CD4 T cells causes DNA damage, cell cycle arrest, and protects from EAE and IBD
PMID: 40540585
5
CLNS1A overexpression in lung cancer promotes chemoresistance through chloride channel activity and FAK-SRC-RAC1 pathway
PMID: 40345428
6
CLNS1A depletion induces detained intron splicing defects and cell cycle loss, indicating PRMT5-splicing axis vulnerability
PMID: 40687829
7
PRMT5-mediated Sm tail methylation via CLNS1A prevents mRNA chromatin retention and promotes nuclear export
PMID: 41086806
Disease Associationsⓘ20
Alzheimer diseaseOpen Targets
0.23Weak
lysosomal storage diseaseOpen Targets
0.23Weak
multiple sclerosisOpen Targets
0.23Weak
neurodegenerative diseaseOpen Targets
0.23Weak
Parkinson diseaseOpen Targets
0.23Weak
Epidermal thickeningOpen Targets
0.19Weak
optic choroid disorderOpen Targets
0.06Suggestive
colon carcinomaOpen Targets
0.04Suggestive
hair colorOpen Targets
0.03Suggestive
neoplasmOpen Targets
0.02Suggestive
breast cancerOpen Targets
0.01Suggestive
experimental autoimmune encephalomyelitisOpen Targets
0.01Suggestive
AutoimmunityOpen Targets
0.01Suggestive
insulinomaOpen Targets
0.01Suggestive
non-small cell lung carcinomaOpen Targets
0.01Suggestive
transitional cell carcinoma of kidneyOpen Targets
0.01Suggestive
multiple myelomaOpen Targets
0.01Suggestive
prostate cancerOpen Targets
0.00Suggestive
infectionOpen Targets
0.00Suggestive
lung cancerOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
SNRPGProtein interaction100%LSM6Protein interaction100%LSM4Protein interaction100%LSM2Protein interaction100%SNRPD1Protein interaction100%SNRPD2Protein interaction100%
Tissue Expression6 tissues
Liver
100%
Brain
94%
Ovary
94%
Bone Marrow
86%
Heart
80%
Lung
44%
Gene Interaction Network
Click a node to explore
CLNS1ASNRPGLSM6LSM4LSM2SNRPD1SNRPD2
PROTEIN STRUCTURE
Preparing viewer…
PDB6V0O · 2.86 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.78LoF Tolerant
pLIⓘ
0.16Tolerant
Observed/Expected LoF0.44 [0.27–0.78]
RankingsWhere CLNS1A stands among ~20K protein-coding genes
  • #3,451of 20,598
    Most Researched134 · top quartile
  • #6,317of 17,882
    Most Constrained (LOEUF)0.78
Genes detectedCLNS1A
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
CLNS1A regulates genome stability and cell cycle progression to control CD4 T cell function and autoimmunity.
PMID: 40540585
Sci Immunol · 2025
1.00
2
Molecular basis for substrate recruitment to the PRMT5 methylosome.
PMID: 34358446
Mol Cell · 2021
0.90
3
Mechanistic insights into CLNS1A-mediated chemoresistance and tumor progression in non-small cell lung cancer.
PMID: 40345428
Cancer Lett · 2025
0.80
4
Characterization of the human gene coding for the swelling-dependent chloride channel ICln at position 11q13.5-14.1 (CLNS1A) and further characterization of the chromosome 6 (CLNS1B) localization.
PMID: 9524223
Gene · 1998
0.70
5
The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing.
PMID: 39763796
bioRxiv · 2024
0.60