Aliases for CLCC1 Gene

Aliases for CLCC1 Gene

  • Chloride Channel CLIC Like 1 2 3 5
  • MCLC 2 3 4
  • Mid-1-Related Chloride Channel Protein 1 3 4
  • Chloride Channel CLIC-Like Protein 1 3 4
  • Mid1-Related Chloride Channel (Yeast) 2
  • Chloride Channel CLIC-Like 1 2
  • KIAA0761 4
  • CLCC1 5
  • RP32 3

External Ids for CLCC1 Gene

Previous GeneCards Identifiers for CLCC1 Gene

  • GC01M109185
  • GC01M108820
  • GC01M109472
  • GC01M107364
  • GC01M108929

Summaries for CLCC1 Gene

GeneCards Summary for CLCC1 Gene

CLCC1 (Chloride Channel CLIC Like 1) is a Protein Coding gene. Diseases associated with CLCC1 include Retinitis Pigmentosa 32 and Retinitis Pigmentosa. Gene Ontology (GO) annotations related to this gene include chloride channel activity.

UniProtKB/Swiss-Prot Summary for CLCC1 Gene

  • Seems to act as a chloride ion channel (PubMed:30157172). Plays a role in retina development (PubMed:30157172).

Gene Wiki entry for CLCC1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLCC1 Gene

Genomics for CLCC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLCC1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J108961 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.3 253 2.7 TBP SP1 MXD4 CEBPA MNT DEK IKZF1 SMAD5 HES1 ZFP64 AKNAD1 CLCC1 PRPF38B C1orf194 WDR47 TAF13 lnc-WDR47-1 GPSM2
GH01J108947 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE 250.4 +15.0 15022 1.6 ZNF341 POU5F1 EGR2 NANOG ZFHX2 CLCC1 TMEM167B ENSG00000270066 lnc-WDR47-1 AKNAD1 GPSM2
GH01J108949 Promoter 0.3 EPDnew 250.4 +13.6 13584 0.1 CLCC1 TMEM167B lnc-WDR47-1 AKNAD1 GPSM2
GH01J108745 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 14.9 +216.4 216402 3.4 CHD2 TBP ZBTB10 MXD4 SP1 MNT DEK IKZF1 SMAD5 HES1 STXBP3 HSALNG0005832 GPR61 CLCC1 WDR47 PRPF38B PSRC1 CELSR2 lnc-STXBP3-2 ENSG00000228076
GH01J109074 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 12.9 -112.2 -112242 2.7 CHD2 TBP MXD4 CEBPA DEK MNT IKZF1 SMAD5 ETS1 HES1 TAF13 RF00017-287 lnc-TMEM167B-2 lnc-TMEM167B-4 ENSG00000258634 PRPF38B RPL17P7 STRIP1 ENSG00000228665 CLCC1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLCC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLCC1

Top Transcription factor binding sites by QIAGEN in the CLCC1 gene promoter:
  • ER-alpha
  • GR
  • GR-alpha
  • GR-beta
  • Hlf
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4

Genomic Locations for CLCC1 Gene

Latest Assembly
36,144 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
33,980 bases
Minus strand

(GRCh37/hg19 by Ensembl)
33,982 bases
Minus strand

Genomic View for CLCC1 Gene

Genes around CLCC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLCC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLCC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCC1 Gene

Proteins for CLCC1 Gene

  • Protein details for CLCC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Chloride channel CLIC-like protein 1
    Protein Accession:
    Secondary Accessions:
    • O94861
    • Q8WYP8
    • Q8WYP9
    • Q9BU25

    Protein attributes for CLCC1 Gene

    551 amino acids
    Molecular mass:
    62023 Da
    Quaternary structure:
    • Interacts with mitochondrial protein PIGBOS1 (via C-terminus); the interaction occurs at the mitochondria-associated endoplasmic reticulum (ER) membrane, a zone of contact between the ER and mitochondrial membranes, but does not appear to play a role in ER-mitochondria tethering and is not affected by ER stress (PubMed:31653868). Interacts with CALR (PubMed:30157172).

    Alternative splice isoforms for CLCC1 Gene


neXtProt entry for CLCC1 Gene

Post-translational modifications for CLCC1 Gene

  • Glycosylation at Thr407, Thr469, and Thr474
  • Ubiquitination at Lys414
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CLCC1 Gene

Domains & Families for CLCC1 Gene

Gene Families for CLCC1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for CLCC1 Gene


Suggested Antigen Peptide Sequences for CLCC1 Gene

GenScript: Design optimal peptide antigens:
  • Mid-1-related chloride channel protein 1 (CLCC1_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the chloride channel MCLC family.
  • Belongs to the chloride channel MCLC family.
genes like me logo Genes that share domains with CLCC1: view

Function for CLCC1 Gene

Molecular function for CLCC1 Gene

UniProtKB/Swiss-Prot Function:
Seems to act as a chloride ion channel (PubMed:30157172). Plays a role in retina development (PubMed:30157172).

Phenotypes From GWAS Catalog for CLCC1 Gene

Gene Ontology (GO) - Molecular Function for CLCC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005254 chloride channel activity IBA 21873635
GO:0005515 protein binding IPI 31653868
genes like me logo Genes that share ontologies with CLCC1: view
genes like me logo Genes that share phenotypes with CLCC1: view

Human Phenotype Ontology for CLCC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLCC1 Gene

MGI Knock Outs for CLCC1:
  • Clcc1 Clcc1<tm1b(KOMP)Mbp>

miRNA for CLCC1 Gene

miRTarBase miRNAs that target CLCC1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCC1

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CLCC1 Gene

Localization for CLCC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCC1 Gene

Endoplasmic reticulum membrane. Multi-pass membrane protein. Golgi apparatus membrane. Multi-pass membrane protein. Nucleus membrane. Multi-pass membrane protein. Note=Within the endoplasmic reticulum (ER), localizes to the mitochondria-associated ER membrane, a zone of contact between the ER and mitochondrial membranes. {ECO:0000269 PubMed:31653868}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLCC1 gene
Compartment Confidence
endoplasmic reticulum 5
nucleus 3
golgi apparatus 3
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLCC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005634 nucleus IEA --
GO:0005783 endoplasmic reticulum IBA,IDA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005794 Golgi apparatus IEA --
genes like me logo Genes that share ontologies with CLCC1: view

Pathways & Interactions for CLCC1 Gene

PathCards logo

SuperPathways for CLCC1 Gene

No Data Available

SIGNOR curated interactions for CLCC1 Gene


Gene Ontology (GO) - Biological Process for CLCC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IEA --
GO:1902476 chloride transmembrane transport IEA --
genes like me logo Genes that share ontologies with CLCC1: view

No data available for Pathways by source for CLCC1 Gene

Drugs & Compounds for CLCC1 Gene

(2) Drugs for CLCC1 Gene - From: PharmGKB and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Chloride ion Experimental Pharma 0
opioids Pharma 0
genes like me logo Genes that share compounds with CLCC1: view

Transcripts for CLCC1 Gene

mRNA/cDNA for CLCC1 Gene

11 NCBI additional mRNA sequence :
30 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCC1

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for CLCC1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - - - -
SP2: - - -
SP4: -
SP6: - -
SP7: - - - -
SP8: - - - -

Relevant External Links for CLCC1 Gene

GeneLoc Exon Structure for

Expression for CLCC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLCC1 Gene

Protein differential expression in normal tissues from HIPED for CLCC1 Gene

This gene is overexpressed in Breast (51.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLCC1 Gene

Protein tissue co-expression partners for CLCC1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLCC1

SOURCE GeneReport for Unigene cluster for CLCC1 Gene:


mRNA Expression by UniProt/SwissProt for CLCC1 Gene:

Tissue specificity: Expressed in the retina of the eye, with extensive expression in the lamina cribrosa, optic nerve, ganglion cell layer, inner nuclear layer, outer nuclear layer and retinal pigment epithelium.

Evidence on tissue expression from TISSUES for CLCC1 Gene

  • Nervous system(4.5)
  • Skin(4.3)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with CLCC1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLCC1 Gene

Orthologs for CLCC1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLCC1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLCC1 30 31
  • 99.4 (n)
(Bos Taurus)
Mammalia CLCC1 30 31
  • 87.64 (n)
(Canis familiaris)
Mammalia CLCC1 30 31
  • 87.44 (n)
(Rattus norvegicus)
Mammalia Clcc1 30
  • 80.96 (n)
(Mus musculus)
Mammalia Clcc1 30 17 31
  • 79.85 (n)
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 68 (a)
-- 31
  • 60 (a)
(Gallus gallus)
Aves CLCC1 30 31
  • 65.24 (n)
(Anolis carolinensis)
Reptilia CLCC1 31
  • 58 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia clcc1 30
  • 59.42 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC397947 30
(Danio rerio)
Actinopterygii LOC100332460 30
  • 52.14 (n)
CLCC1 31
  • 35 (a)
Species where no ortholog for CLCC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CLCC1 Gene

Gene Tree for CLCC1 (if available)
Gene Tree for CLCC1 (if available)
Evolutionary constrained regions (ECRs) for CLCC1: view image

Paralogs for CLCC1 Gene

No data available for Paralogs for CLCC1 Gene

Variants for CLCC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLCC1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
835612 Uncertain Significance: not provided 108,934,878(-) G/A
NM_001377458.1(CLCC1):c.1448C>T (p.Pro483Leu)
837514 Uncertain Significance: not provided 108,941,460(-) C/T
NM_001048210.3(CLCC1):c.741G>A (p.Met247Ile)
843901 Uncertain Significance: not provided 108,937,133(-) G/A
NM_001048210.3(CLCC1):c.1327C>T (p.Arg443Trp)
845469 Uncertain Significance: not provided 108,934,726(-) C/T
NM_001377458.1(CLCC1):c.1600G>A (p.Ala534Thr)
846256 Uncertain Significance: not provided 108,939,750(-) C/T
NM_001048210.3(CLCC1):c.927G>A (p.Thr309=)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLCC1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CLCC1 Gene

Variant ID Type Subtype PubMed ID
dgv15n21 CNV gain 19592680
dgv251n100 CNV loss 25217958
esv2421924 CNV deletion 20811451
esv24963 CNV loss 19812545
esv2662481 CNV deletion 23128226
esv2715940 CNV deletion 23290073
esv2760082 CNV loss 21179565
esv3567237 CNV deletion 23714750
esv3587142 CNV loss 21293372
esv3587143 CNV loss 21293372
nsv1137793 CNV deletion 24896259
nsv437236 CNV loss 16327808
nsv441708 CNV loss 18776908
nsv514000 CNV loss 21397061
nsv526049 CNV loss 19592680
nsv547425 CNV gain 21841781
nsv831026 CNV loss 17160897

Variation tolerance for CLCC1 Gene

Residual Variation Intolerance Score: 54.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.51; 77.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLCC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCC1 Gene

Disorders for CLCC1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CLCC1 Gene - From: OMI, CVR, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search CLCC1 in MalaCards View complete list of genes associated with diseases


  • Retinitis pigmentosa 32 (RP32) [MIM:609913]: A form of retinitis pigmentosa, a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. RP32 inheritance is autosomal recessive. {ECO:0000269 PubMed:16189710, ECO:0000269 PubMed:30157172}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for CLCC1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CLCC1: view

No data available for Genatlas for CLCC1 Gene

Publications for CLCC1 Gene

  1. Identification of a novel chloride channel expressed in the endoplasmic reticulum, golgi apparatus, and nucleus. (PMID: 11279057) Nagasawa M … Kojima I (The Journal of biological chemistry 2001) 2 3 4 23
  2. Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa. (PMID: 30157172) Li L … Hejtmancik JF (PLoS genetics 2018) 3 4 74
  3. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9872452) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4
  4. Regulation of the ER stress response by a mitochondrial microprotein. (PMID: 31653868) Chu Q … Saghatelian A (Nature communications 2019) 3 4
  5. Identification of type 2 diabetes-associated combination of SNPs using support vector machine. (PMID: 20416077) Ban HJ … Park KJ (BMC genetics 2010) 3 41

Products for CLCC1 Gene

Sources for CLCC1 Gene