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

Gene ID: 23155, updated on 3-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
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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 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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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

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