CLNS1A

chloride nucleotide-sensitive channel 1A

Basic information

Region (hg38): 11:77514935-77637794

Previous symbols: [ "CLCI" ]

Links

ENSG00000074201 ∙ NCBI:1207 ∙ OMIM:602158 ∙ HGNC:2080 ∙ Uniprot:P54105 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLNS1A gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLNS1A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in CLNS1A

This is a list of pathogenic ClinVar variants found in the CLNS1A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-77590014-C-G		not specified	Uncertain significance (Oct 27, 2022)
11-77590015-G-C		not specified	Uncertain significance (Nov 09, 2021)
11-77590055-G-T		not specified	Uncertain significance (May 09, 2023)
11-77590113-A-G		not specified	Uncertain significance (Dec 20, 2021)
11-77590254-G-T		not specified	Uncertain significance (Mar 31, 2023)
11-77590291-C-T		not specified	Uncertain significance (Sep 27, 2022)
11-77590377-C-A		not specified	Uncertain significance (Nov 27, 2023)
11-77590426-A-C			Likely benign (Jan 01, 2023)
11-77590427-G-T			Likely benign (Jan 01, 2023)
11-77590448-C-A		not specified	Uncertain significance (May 24, 2023)
11-77590464-C-G		not specified	Uncertain significance (May 10, 2023)
11-77590464-C-T			Uncertain significance (Nov 26, 2018)
11-77590506-G-A		not specified	Likely benign (Feb 05, 2024)
11-77590530-G-A		not specified	Uncertain significance (Aug 10, 2023)
11-77590548-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-77590596-T-C		not specified	Uncertain significance (Jan 04, 2024)
11-77590605-T-C		not specified	Uncertain significance (Nov 05, 2021)
11-77609341-G-T			Uncertain significance (Nov 26, 2018)
11-77619695-T-C		not specified	Uncertain significance (Mar 11, 2024)
11-77622539-C-A		not specified	Uncertain significance (Apr 26, 2023)
11-77622619-T-A		not specified	Uncertain significance (Aug 09, 2021)
11-77622654-G-C		not specified	Uncertain significance (Jul 25, 2023)
11-77624980-T-C		not specified	Uncertain significance (Nov 19, 2022)
11-77625044-C-G		not specified	Uncertain significance (Feb 22, 2023)
11-77629855-T-C		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLNS1A	protein_coding	protein_coding	ENST00000525428	6	122870

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0814	0.909	125711	0	35	125746	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.882	96	124	0.777	0.00000573	1547
Missense in Polyphen		14	25.601	0.54685		346
Synonymous	0.717	40	46.2	0.866	0.00000220	436
Loss of Function	2.27	4	12.7	0.314	6.23e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000217
Finnish	0.000205	0.000185
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.000221	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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. {ECO:0000269|PubMed:10330151, ECO:0000269|PubMed:11713266, ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:21081503}.
• Pathway: RNA transport - Homo sapiens (human);snRNP Assembly;Metabolism of RNA;Metabolism of non-coding RNA (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.609
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.687
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Clns1a
• Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: clns1a
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: branchiness

Gene ontology

• Biological process: spliceosomal snRNP assembly;chloride transport;cell volume homeostasis
• Cellular component: nucleus;nucleoplasm;cytosol;cytoskeleton;plasma membrane;methylosome;pICln-Sm protein complex
• Molecular function: RNA binding;protein binding;protein heterodimerization activity