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    CLCC1 chloride channel CLIC like 1 [ Homo sapiens (human) ]

    Gene ID: 23155, updated on 27-Nov-2024

    Summary

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    Official Symbol
    CLCC1provided by HGNC
    Official Full Name
    chloride channel CLIC like 1provided by HGNC
    Primary source
    HGNC:HGNC:29675
    See related
    Ensembl:ENSG00000121940 MIM:617539; AllianceGenome:HGNC:29675
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MCLC; RP32; ERAC1
    Summary
    Enables chloride channel activity. Involved in endoplasmic reticulum calcium ion homeostasis. Located in endoplasmic reticulum membrane and mitochondria-associated endoplasmic reticulum membrane contact site. Implicated in retinitis pigmentosa 32. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 9.3), thyroid (RPKM 9.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLCC1 in Genome Data Viewer
    Location:
    1p13.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (108929505..108963484, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (108962861..108996846, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (109472127..109506106, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378891 Neighboring gene AKNA domain containing 1 Neighboring gene Sharpr-MPRA regulatory region 12963 Neighboring gene spermatogenesis associated 42 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1139 Neighboring gene G protein signaling modulator 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109500895-109501396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109503808-109504308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109504309-109504809 Neighboring gene Sharpr-MPRA regulatory region 7966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1140 Neighboring gene NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-like Neighboring gene WD repeat domain 47 Neighboring gene ribosomal protein L17 pseudogene 7

    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. Chloride channels and hepatocellular function: prospects for molecular identification. Li X, et al. Annu Rev Physiol, 2002. PMID 11826282
    2. Mutation and clinical analysis of the CLCC1 gene in amyotrophic lateral sclerosis patients from Central South China. Tang L, et al. Ann Clin Transl Neurol, 2024 Jan. PMID 37916886, Free PMC Article
    3. Severe autosomal recessive retinitis pigmentosa maps to chromosome 1p13.3-p21.2 between D1S2896 and D1S457 but outside ABCA4. Zhang Q, et al. Hum Genet, 2005 Dec. PMID 16189710
    4. Unraveling the CLCC1 interactome: Impact of the Asp25Glu variant and its interaction with SigmaR1 at the Mitochondrial-Associated ER Membrane (MAM). D'Atri I, et al. Neurosci Lett, 2024 May 1. PMID 38621504
    5. Identification of a novel chloride channel expressed in the endoplasmic reticulum, golgi apparatus, and nucleus. Nagasawa M, et al. J Biol Chem, 2001 Jun 8. PMID 11279057

    See all (87) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Unraveling the CLCC1 interactome: Impact of the Asp25Glu variant and its interaction with SigmaR1 at the Mitochondrial-Associated ER Membrane (MAM).
      Title: Unraveling the CLCC1 interactome: Impact of the Asp25Glu variant and its interaction with SigmaR1 at the Mitochondrial-Associated ER Membrane (MAM).
    2. Mutation and clinical analysis of the CLCC1 gene in amyotrophic lateral sclerosis patients from Central South China.
      Title: Mutation and clinical analysis of the CLCC1 gene in amyotrophic lateral sclerosis patients from Central South China.
    3. Intracellular chloride transport by CLCC1 is a critical process in maintaining retinal integrity, and CLCC1 is crucial for survival and function of retinal cells.
      Title: Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa.
    4. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Identification of type 2 diabetes-associated combination of SNPs using support vector machine.
    Submit: New GeneRIF Correction

    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

    Associated conditions

    Description Tests
    Retinitis pigmentosa 32
    MedGen: C1835927 OMIM: 609913 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genes linked to energy metabolism and immunoregulatory mechanisms are associated with subcutaneous adipose tissue distribution in HIV-infected men.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: AKNAD1

    Homology

    Clone Names

    • FLJ57956, KIAA0761

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chloride channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chloride channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endoplasmic reticulum calcium ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of chloride channel complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane HDA PubMed 
    located_in mitochondria-associated endoplasmic reticulum membrane contact site IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    chloride channel CLIC-like protein 1
    Names
    ER anion channel 1
    Mid-1-related chloride channel protein 1
    retinitis pigmentosa 32 (autosomal recessive)

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001048210.3 → NP_001041675.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001041675.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000510352.1, ENST00000685540.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    2. NM_001278202.2 → NP_001265131.1  chloride channel CLIC-like protein 1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001265131.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks two consecutive exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS60215.1
      UniProtKB/TrEMBL
      A0A6Q8PGA4
      Related
      ENSP00000510524.1, ENST00000688610.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 430
      MCLC; Mid-1-related chloride channel (MCLC)

    3. NM_001278203.1 → NP_001265132.1  chloride channel CLIC-like protein 1 isoform 4 precursor

      See identical proteins and their annotated locations for NP_001265132.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks four consecutive exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AB018304, AB052918, AL449266, BQ685798
      Consensus CDS
      CCDS60214.1
      UniProtKB/Swiss-Prot
      Q96S66
      Related
      ENSP00000337243.2, ENST00000348264.6
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 366
      MCLC; Mid-1-related chloride channel (MCLC)

    4. NM_001377458.1 → NP_001364387.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000358986.3, ENST00000369969.7
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    5. NM_001377459.1 → NP_001364388.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000509451.1, ENST00000691556.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    6. NM_001377460.1 → NP_001364389.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000510137.1, ENST00000690781.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    7. NM_001377461.1 → NP_001364390.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000349456.2, ENST00000356970.6
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    8. NM_001377462.1 → NP_001364391.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000510675.1, ENST00000689189.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    9. NM_001377463.1 → NP_001364392.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000510715.1, ENST00000688778.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    10. NM_001377464.1 → NP_001364393.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000502457.1, ENST00000675956.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    11. NM_001377465.1 → NP_001364394.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000508563.1, ENST00000686821.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    12. NM_001377466.1 → NP_001364395.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000510579.1, ENST00000687134.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    13. NM_001377467.1 → NP_001364396.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000509584.1, ENST00000691513.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    14. NM_001377468.1 → NP_001364397.1  chloride channel CLIC-like protein 1 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS41362.1
      UniProtKB/Swiss-Prot
      O94861, Q8WYP8, Q8WYP9, Q96S66, Q9BU25
      UniProtKB/TrEMBL
      A0A6Q8PEZ7
      Related
      ENSP00000509218.1, ENST00000687865.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 551
      MCLC; Mid-1-related chloride channel (MCLC)

    15. NM_001377469.1 → NP_001364398.1  chloride channel CLIC-like protein 1 isoform 5 precursor

      Status: VALIDATED

      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS91013.1
      UniProtKB/TrEMBL
      A0A6Q8PEZ7, A0A6Q8PG14
      Related
      ENSP00000502042.2, ENST00000675247.2
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 517
      MCLC; Mid-1-related chloride channel (MCLC)

    16. NM_001377470.1 → NP_001364399.1  chloride channel CLIC-like protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL449266
      UniProtKB/TrEMBL
      A0A6Q8PFF7
      Related
      ENSP00000501777.1, ENST00000675018.1
      Conserved Domains (1) summary
      pfam05934
      Location:17 → 454
      MCLC; Mid-1-related chloride channel (MCLC)

    17. NM_015127.5 → NP_055942.1  chloride channel CLIC-like protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_055942.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses alternate splice sites in the 5' UTR and in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL449266
      Consensus CDS
      CCDS793.1
      UniProtKB/TrEMBL
      A0A6Q8PGA4
      Related
      ENSP00000508570.1, ENST00000686434.1
      Conserved Domains (1) summary
      pfam05934
      Location:14 → 501
      MCLC; Mid-1-related chloride channel (MCLC)

    RNA

    1. NR_165299.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL449266

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      108929505..108963484 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      108962861..108996846 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96S66.1 GenPept UniProtKB/Swiss-Prot:Q96S66

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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