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Aliases for CIC Gene

Aliases for CIC Gene

  • Capicua Transcriptional Repressor 2 3 5
  • Capicua (Drosophila) Homolog 2
  • Capicua Homolog (Drosophila) 2
  • Protein Capicua Homolog 3
  • KIAA0306 4
  • MRD45 3

External Ids for CIC Gene

Previous GeneCards Identifiers for CIC Gene

  • GC19P043435
  • GC19P043180
  • GC19P047454
  • GC19P047480
  • GC19P042788
  • GC19P039219
  • GC19P042772

Summaries for CIC Gene

Entrez Gene Summary for CIC Gene

  • The protein encoded by this gene is an ortholog of the Drosophila melanogaster capicua gene, and is a member of the high mobility group (HMG)-box superfamily of transcriptional repressors. This protein contains a conserved HMG domain that is involved in DNA binding and nuclear localization, and a conserved C-terminus. Studies suggest that the N-terminal region of this protein interacts with Atxn1 (GeneID:6310), to form a transcription repressor complex, and in vitro studies suggest that polyglutamine-expansion of ATXN1 may alter the repressor activity of this complex. Mutations in this gene have been associated with olidogdendrogliomas (PMID:21817013). In addition, translocation events resulting in gene fusions of this gene with both DUX4 (GeneID:100288687) and FOXO4 (GeneID:4303) have been associated with round cell sarcomas. There are multiple pseudogenes of this gene found on chromosomes 1, 4, 6, 7, 16, 20, and the Y chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]

CIViC summary for CIC Gene

GeneCards Summary for CIC Gene

CIC (Capicua Transcriptional Repressor) is a Protein Coding gene. Diseases associated with CIC include Mental Retardation, Autosomal Dominant 45 and Autosomal Dominant Non-Syndromic Intellectual Disability. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is BBX.

UniProtKB/Swiss-Prot for CIC Gene

  • Transcriptional repressor which plays a role in development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, involved in brain development.

Gene Wiki entry for CIC Gene

Additional gene information for CIC Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CIC Gene

Genomics for CIC Gene

GeneHancer (GH) Regulatory Elements for CIC Gene

Promoters and enhancers for CIC 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
GH19J042267 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 653.3 +2.4 2351 6.9 MLX FEZF1 YBX1 YY1 SLC30A9 E2F8 ZNF143 ZNF548 SP3 NFYC CIC PIR59110 ZNF526 ZNF574 CCDC97 DEDD2 MEGF8 CEACAM3 PAFAH1B3 PRR19
GH19J041348 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 33.7 -916.9 -916924 6.9 HDGF PKNOX1 ZFP64 ARID4B SIN3A YBX1 DMAP1 IRF4 YY1 ZNF213 TMEM91 ENSG00000255730 TGFB1 ZNF526 SNRPA ZNF574 HNRNPUL1 CCDC97 ENSG00000269843 COQ8B
GH19J041294 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.1 -965.2 -965240 16.8 CLOCK MLX ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 CCDC97 ZNF526 HNRNPUL1 SNRPA ZNF574 ENSG00000269843 COQ8B TGFB1 AXL ITPKC
GH19J042276 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 14.5 +13.4 13376 11.1 YBX1 E2F8 ZNF416 ZNF143 SP3 NFYC ZFP41 SSRP1 ZNF610 GLIS1 ZNF526 ZNF574 CCDC97 MEGF8 CEACAMP1 CEACAMP10 CIC PSG6 GRIK5 DEDD2
GH19J041882 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.9 -381.9 -381878 9.2 MLX FEZF1 DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF548 ARHGEF1 ZNF526 CCDC97 HNRNPUL1 ZNF574 RPS19 RABAC1 ENSG00000271299 CEACAMP1 CYP2G2P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CIC on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CIC gene promoter:
  • GATA-1
  • c-Myb
  • Roaz
  • AREB6
  • TBP
  • deltaCREB
  • CREB
  • Ik-3

Genomic Locations for CIC Gene

Genomic Locations for CIC Gene
27,261 bases
Plus strand
27,261 bases
Plus strand

Genomic View for CIC Gene

Genes around CIC on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CIC Gene

Proteins for CIC Gene

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

    Protein Symbol:
    Recommended name:
    Protein capicua homolog
    Protein Accession:
    Secondary Accessions:
    • Q7LGI1
    • Q9UEG5
    • Q9Y6T1

    Protein attributes for CIC Gene

    1608 amino acids
    Molecular mass:
    163820 Da
    Quaternary structure:
    • Interacts with ATXN1 and ATXN1L. Found in a complex with ATXN1 and ATXN1L.
    • Expressed in medulloblastoma, a pediatric brain tumor which may arise from the granule cell lineage.
    • Sequence=AAD11988.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CIC Gene

neXtProt entry for CIC Gene

Post-translational modifications for CIC Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CIC Gene

Domains & Families for CIC Gene

Gene Families for CIC Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for CIC Gene

Suggested Antigen Peptide Sequences for CIC Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CIC: view

No data available for UniProtKB/Swiss-Prot for CIC Gene

Function for CIC Gene

Molecular function for CIC Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor which plays a role in development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, involved in brain development.

Phenotypes From GWAS Catalog for CIC Gene

Gene Ontology (GO) - Molecular Function for CIC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 16713569
genes like me logo Genes that share ontologies with CIC: view
genes like me logo Genes that share phenotypes with CIC: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CIC Gene

Localization for CIC Gene

Subcellular locations from UniProtKB/Swiss-Prot for CIC Gene


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 CIC gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CIC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005654 nucleoplasm IDA --
GO:0032991 protein-containing complex IEA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with CIC: view

Pathways & Interactions for CIC Gene

No Data Available

SIGNOR curated interactions for CIC Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for CIC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007420 brain development ISS,IEA --
GO:0007612 learning IEA,ISS --
genes like me logo Genes that share ontologies with CIC: view

No data available for Pathways by source for CIC Gene

Drugs & Compounds for CIC Gene

(1) Drugs for CIC Gene - From: ClinicalTrials

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Gastrointestinal Agents Pharma 8904
genes like me logo Genes that share compounds with CIC: view

Transcripts for CIC Gene

mRNA/cDNA for CIC Gene

Unigene Clusters for CIC Gene

Capicua transcriptional repressor:
Representative Sequences:

Clone Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b · 16c ^ 17 ^ 18 ^ 19 ^ 20

Relevant External Links for CIC Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CIC Gene

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

Protein differential expression in normal tissues from HIPED for CIC Gene

This gene is overexpressed in Pancreas (16.3), Peripheral blood mononuclear cells (14.5), and Fetal testis (7.7).

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

Protein tissue co-expression partners for CIC Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CIC Gene:


SOURCE GeneReport for Unigene cluster for CIC Gene:


mRNA Expression by UniProt/SwissProt for CIC Gene:

Tissue specificity: Expressed in fetal brain.

Evidence on tissue expression from TISSUES for CIC Gene

  • Nervous system(4.5)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with CIC: view

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 CIC Gene

Orthologs for CIC Gene

This gene was present in the common ancestor of animals.

Orthologs for CIC Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CIC 34 33
  • 99.59 (n)
(Canis familiaris)
Mammalia CIC 34 33
  • 90.22 (n)
(Rattus norvegicus)
Mammalia Cic 33
  • 87.97 (n)
(Mus musculus)
Mammalia Cic 16 34 33
  • 87.72 (n)
(Monodelphis domestica)
Mammalia CIC 34
  • 69 (a)
(Bos Taurus)
Mammalia CIC 34
  • 59 (a)
(Anolis carolinensis)
Reptilia CIC 34
  • 17 (a)
(Danio rerio)
Actinopterygii cicb 34
  • 23 (a)
cica 34
  • 22 (a)
Dr.13863 33
fruit fly
(Drosophila melanogaster)
Insecta cic 34 35
  • 11 (a)
bbx 34
  • 8 (a)
(Caenorhabditis elegans)
Secernentea gei-3 34 35
  • 15 (a)
Species where no ortholog for CIC was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for CIC Gene

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

Paralogs for CIC Gene

Paralogs for CIC Gene

(7) SIMAP similar genes for CIC Gene using alignment to 6 proteins:

  • I3L135_HUMAN
  • I3L1Q4_HUMAN
  • I3L2I4_HUMAN
  • I3L2J0_HUMAN
  • I3L373_HUMAN
genes like me logo Genes that share paralogs with CIC: view

Variants for CIC Gene

Sequence variations from dbSNP and Humsavar for CIC Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs373584239 pathogenic, MENTAL RETARDATION, AUTOSOMAL DOMINANT 45 42,290,242(+) C/A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant, synonymous_variant
rs770323488 A breast cancer sample 42,290,722(+) G/A/C coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs797044893 uncertain-significance, Inborn genetic diseases 42,292,968(+) C/T 3_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant
VAR_035936 A breast cancer sample p.Glu104Lys
VAR_065090 Mental retardation, autosomal dominant 45 (MRD45) [MIM:617600] p.Arg492Trp

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

Variant ID Type Subtype PubMed ID
esv2422471 CNV deletion 17116639
esv28255 CNV gain 19812545
nsv1160627 CNV deletion 26073780
nsv520239 CNV loss 19592680
nsv522854 CNV gain 19592680
nsv526186 CNV gain 19592680
nsv833834 CNV loss 17160897
nsv953583 CNV deletion 24416366

Variation tolerance for CIC Gene

Residual Variation Intolerance Score: 0.452% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.22; 52.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CIC Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for CIC Gene

MalaCards: The human disease database

(5) MalaCards diseases for CIC Gene - From: HGMD, OMIM, ClinVar, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, autosomal dominant 45
  • mrd45
autosomal dominant non-syndromic intellectual disability
  • autosomal dominant mental retardation
superficial mycosis
  • piedra
spinocerebellar ataxia 1
  • sca1
  • oligodendroglial neoplasm
- elite association - COSMIC cancer census association via MalaCards
Search CIC in MalaCards View complete list of genes associated with diseases


  • Mental retardation, autosomal dominant 45 (MRD45) [MIM:617600]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD45 patients manifest developmental delay, variable intellectual disability, and behavioral disorders, including autistic features, attention deficit, and hyperactivity. {ECO:0000269 PubMed:21076407, ECO:0000269 PubMed:28288114}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CIC

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

No data available for Genatlas for CIC Gene

Publications for CIC Gene

  1. CIC, a gene involved in cerebellar development and ErbB signaling, is significantly expressed in medulloblastomas. (PMID: 15981098) Lee CJ … Scotting PJ (Journal of neuro-oncology 2005) 2 3 4 58
  2. CIC, a member of a novel subfamily of the HMG-box superfamily, is transiently expressed in developing granule neurons. (PMID: 12393275) Lee CJ … Scotting PJ (Brain research. Molecular brain research 2002) 2 3 4 58
  3. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. (PMID: 28288114) Lu HC … Zoghbi HY (Nature genetics 2017) 3 4 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58

Products for CIC Gene

Sources for CIC Gene

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