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Aliases for ZIC1 Gene

Aliases for ZIC1 Gene

  • Zic Family Member 1 2 3 5
  • Zic Family Member 1 (Odd-Paired Homolog, Drosophila) 2 3
  • Zinc Finger Protein Of The Cerebellum 1 3 4
  • Zinc Finger Protein 201 3 4
  • ZNF201 3 4
  • ZIC 3 4
  • Zic Family Member 1 (Odd-Paired Drosophila Homolog) 2
  • Zinc Finger Protein ZIC 1 3
  • CRS6 3

External Ids for ZIC1 Gene

Previous GeneCards Identifiers for ZIC1 Gene

  • GC03P143961
  • GC03P148012
  • GC03P148408
  • GC03P148448
  • GC03P148609
  • GC03P147111
  • GC03P144503

Summaries for ZIC1 Gene

Entrez Gene Summary for ZIC1 Gene

  • This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. Members of this family are important during development. Aberrant expression of this gene is seen in medulloblastoma, a childhood brain tumor. This gene is closely linked to the gene encoding zinc finger protein of the cerebellum 4, a related family member on chromosome 3. This gene encodes a transcription factor that can bind and transactivate the apolipoprotein E gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for ZIC1 Gene

ZIC1 (Zic Family Member 1) is a Protein Coding gene. Diseases associated with ZIC1 include Craniosynostosis 6 and Isolated Oxycephaly. Among its related pathways are Neural Crest Differentiation and Differentiation of white and brown adipocyte. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity. An important paralog of this gene is ZIC2.

UniProtKB/Swiss-Prot for ZIC1 Gene

  • Acts as a transcriptional activator. Involved in neurogenesis. Plays important roles in the early stage of organogenesis of the CNS, as well as during dorsal spinal cord development and maturation of the cerebellum. Involved in the spatial distribution of mossy fiber (MF) neurons within the pontine gray nucleus (PGN). Plays a role in the regulation of MF axon pathway choice. Promotes MF migration towards ipsilaterally-located cerebellar territories. May have a role in shear flow mechanotransduction in osteocytes. Retains nuclear GLI1 and GLI3 in the cytoplasm. Binds to the minimal GLI-consensus sequence 5-TGGGTGGTC-3 (By similarity).

Gene Wiki entry for ZIC1 Gene

Additional gene information for ZIC1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZIC1 Gene

Genomics for ZIC1 Gene

GeneHancer (GH) Regulatory Elements for ZIC1 Gene

Promoters and enhancers for ZIC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I147407 Promoter/Enhancer 1.8 VISTA EPDnew ENCODE dbSUPER 554.6 +16.3 16346 4.8 RING1 MXI1 PKNOX1 USF1 SUZ12 MAX SIN3A ZNF384 FOXM1 POLR2A ZIC1 ZIC4 LOC440982
GH03I147391 Enhancer 0.9 ENCODE dbSUPER 550.8 +0.1 51 3.2 CTCF PKNOX1 SUZ12 MAX SIN3A BMI1 RAD21 RFX5 YY1 POLR2A ZIC1 ENSG00000243620 ZIC4
GH03I147419 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 38.3 +25.9 25893 0.2 ZNF639 MEIS2 MXI1 USF1 L3MBTL2 ZBTB2 SUZ12 BHLHE40 NRF1 MAX ZIC1 ZIC4 ZIC4-AS1 ENSG00000243620 LOC440982
GH03I147424 Enhancer 0.7 FANTOM5 dbSUPER 28.1 +31.1 31099 0.2 CTBP2 EZH2 ZIC1 ZIC4-AS1 ZIC4 ENSG00000243620 LOC440982 NPM1P28
GH03I147415 Enhancer 0.8 UCNEbase dbSUPER 12.6 +21.9 21919 0.2 POLR2A EZH2 ZIC1 ENSG00000243620 LOC440982 ZIC4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZIC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZIC1 gene promoter:

Genomic Locations for ZIC1 Gene

Genomic Locations for ZIC1 Gene
chr3:147,393,422-147,510,293
(GRCh38/hg38)
Size:
116,872 bases
Orientation:
Plus strand
chr3:147,111,209-147,228,080
(GRCh37/hg19)

Genomic View for ZIC1 Gene

Genes around ZIC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZIC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZIC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZIC1 Gene

Proteins for ZIC1 Gene

  • Protein details for ZIC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15915-ZIC1_HUMAN
    Recommended name:
    Zinc finger protein ZIC 1
    Protein Accession:
    Q15915
    Secondary Accessions:
    • Q2M3N1

    Protein attributes for ZIC1 Gene

    Size:
    447 amino acids
    Molecular mass:
    48309 Da
    Quaternary structure:
    • Interacts (via the C2H2-type domains 3, 4 and 5) with MDFIC (via the C2H2-type domains 3, 4 and 5). Interacts with GLI1; the interaction enhances transcription activation. Interacts with GLI2. Interacts with GLI3; the interaction enhances transcription activation (By similarity).

neXtProt entry for ZIC1 Gene

Post-translational modifications for ZIC1 Gene

No Post-translational modifications

Other Protein References for ZIC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZIC1 Gene

Domains & Families for ZIC1 Gene

Gene Families for ZIC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ZIC1 Gene

Suggested Antigen Peptide Sequences for ZIC1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q15915

UniProtKB/Swiss-Prot:

ZIC1_HUMAN :
  • The C2H2-type 3, 4 and 5 zinc finger domains are necessary for transcription activation.
  • Belongs to the GLI C2H2-type zinc-finger protein family.
Domain:
  • The C2H2-type 3, 4 and 5 zinc finger domains are necessary for transcription activation.
Family:
  • Belongs to the GLI C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with ZIC1: view

Function for ZIC1 Gene

Molecular function for ZIC1 Gene

GENATLAS Biochemistry:
zinc finger protein of the cerebellum,mouse Zic homolog,potential marker for medulloblastoma and cellular granular cell lineage
UniProtKB/Swiss-Prot Function:
Acts as a transcriptional activator. Involved in neurogenesis. Plays important roles in the early stage of organogenesis of the CNS, as well as during dorsal spinal cord development and maturation of the cerebellum. Involved in the spatial distribution of mossy fiber (MF) neurons within the pontine gray nucleus (PGN). Plays a role in the regulation of MF axon pathway choice. Promotes MF migration towards ipsilaterally-located cerebellar territories. May have a role in shear flow mechanotransduction in osteocytes. Retains nuclear GLI1 and GLI3 in the cytoplasm. Binds to the minimal GLI-consensus sequence 5-TGGGTGGTC-3 (By similarity).

Phenotypes From GWAS Catalog for ZIC1 Gene

Gene Ontology (GO) - Molecular Function for ZIC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA,TAS 8542595
genes like me logo Genes that share ontologies with ZIC1: view
genes like me logo Genes that share phenotypes with ZIC1: view

Human Phenotype Ontology for ZIC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ZIC1 Gene

MGI Knock Outs for ZIC1:

Transcription Factor Targets for ZIC1 Gene

Selected GeneGlobe predicted Target genes for ZIC1
Targeted motifs for ZIC1 Gene
HOMER Transcription Factor Regulatory Elements motif ZIC1
  • Consensus sequence: CCTGCTGAGH Submotif: canonical Cell Type: Cerebellum GEO ID: GSE60731

Clone Products

No data available for Enzyme Numbers (IUBMB) for ZIC1 Gene

Localization for ZIC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZIC1 Gene

Nucleus. Cytoplasm. Note=Localizes in the cytoplasm in presence of MDFIC overexpression. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
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 ZIC1 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ZIC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 8542595
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with ZIC1: view

Pathways & Interactions for ZIC1 Gene

genes like me logo Genes that share pathways with ZIC1: view

Pathways by source for ZIC1 Gene

SIGNOR curated interactions for ZIC1 Gene

Activates:

Gene Ontology (GO) - Biological Process for ZIC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
GO:0007389 pattern specification process ISS,IEA --
genes like me logo Genes that share ontologies with ZIC1: view

Drugs & Compounds for ZIC1 Gene

(1) Drugs for ZIC1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with ZIC1: view

Transcripts for ZIC1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZIC1 Gene

No ASD Table

Relevant External Links for ZIC1 Gene

GeneLoc Exon Structure for
ZIC1
ECgene alternative splicing isoforms for
ZIC1

Expression for ZIC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZIC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ZIC1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x24.4) and Brain - Cerebellum (x18.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ZIC1 Gene



Protein tissue co-expression partners for ZIC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZIC1 Gene:

ZIC1

SOURCE GeneReport for Unigene cluster for ZIC1 Gene:

Hs.598590

mRNA Expression by UniProt/SwissProt for ZIC1 Gene:

Q15915-ZIC1_HUMAN
Tissue specificity: CNS. A high level expression is seen in the cerebellum. Detected in the nuclei of the cerebellar granule cell lineage from the progenitor cells of the external germinal layer to the postmigrated cells of the internal granular layer. Detected in medulloblastoma (26/29 cases), but not present in all other tumors examined.

Evidence on tissue expression from TISSUES for ZIC1 Gene

  • Nervous system(4.8)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ZIC1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • meninges
  • skull
General:
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with ZIC1: view

No data available for Protein differential expression in normal tissues for ZIC1 Gene

Orthologs for ZIC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZIC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZIC1 33 34
  • 99.85 (n)
cow
(Bos Taurus)
Mammalia ZIC1 33 34
  • 93.3 (n)
oppossum
(Monodelphis domestica)
Mammalia ZIC1 34
  • 92 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Zic1 33
  • 91.2 (n)
mouse
(Mus musculus)
Mammalia Zic1 33 16 34
  • 90.83 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ZIC1 34
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves ZIC1 33 34
  • 81.98 (n)
lizard
(Anolis carolinensis)
Reptilia ZIC1 34
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia zic1 33
  • 78.81 (n)
Str.17224 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.1796 33
zebrafish
(Danio rerio)
Actinopterygii zic1 33 34
  • 76.32 (n)
fruit fly
(Drosophila melanogaster)
Insecta opa 35 34
  • 66 (a)
lmd 35
  • 45 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 38 (a)
ManyToMany
Species where no ortholog for ZIC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • dog (Canis familiaris)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 ZIC1 Gene

ENSEMBL:
Gene Tree for ZIC1 (if available)
TreeFam:
Gene Tree for ZIC1 (if available)

Paralogs for ZIC1 Gene

Variants for ZIC1 Gene

Sequence variations from dbSNP and Humsavar for ZIC1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1057517667 pathogenic, Craniosynostosis 6 147,413,370(+) C/A coding_sequence_variant, stop_gained
rs1057517668 pathogenic, Craniosynostosis 6 147,413,372(+) C/T coding_sequence_variant, stop_gained
rs1057517669 pathogenic, Craniosynostosis 6 147,413,411(+) G/T coding_sequence_variant, stop_gained
rs1057517670 pathogenic, Craniosynostosis 6, 6 (CRS6) [MIM:616602] 147,413,405(+) G/C coding_sequence_variant, missense_variant
rs1064794698 likely-pathogenic, not provided 147,412,627(+) C/A/T coding_sequence_variant, stop_gained, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for ZIC1 Gene

Variant ID Type Subtype PubMed ID
nsv822285 CNV gain 20364138
nsv954489 CNV deletion 24416366

Variation tolerance for ZIC1 Gene

Residual Variation Intolerance Score: 17.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.26; 5.84% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZIC1 Gene

Human Gene Mutation Database (HGMD)
ZIC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZIC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZIC1 Gene

Disorders for ZIC1 Gene

MalaCards: The human disease database

(20) MalaCards diseases for ZIC1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
craniosynostosis 6
  • crs6
isolated oxycephaly
  • acrocephaly
isolated brachycephaly
  • non-syndromic bicoronal synostosis
isolated plagiocephaly
  • craniosynostosis
medulloblastoma
  • mdb
- elite association - COSMIC cancer census association via MalaCards
Search ZIC1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

ZIC1_HUMAN
  • Craniosynostosis 6 (CRS6) [MIM:616602]: A form of craniosynostosis, a primary abnormality of skull growth involving premature fusion of one or more cranial sutures. The growth velocity of the skull often cannot match that of the developing brain resulting in an abnormal head shape and, in some cases, increased intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability. {ECO:0000269 PubMed:26340333}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for ZIC1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ZIC1: view

No data available for Genatlas for ZIC1 Gene

Publications for ZIC1 Gene

  1. Predominant expression of human zic in cerebellar granule cell lineage and medulloblastoma. (PMID: 8542595) Yokota N … Mikoshiba K (Cancer research 1996) 2 3 4 22 58
  2. Genetic variants in ZIC1, ZIC2, and ZIC3 are not major risk factors for neural tube defects in humans. (PMID: 14679585) Klootwijk R … Franke B (American journal of medical genetics. Part A 2004) 3 22 44 58
  3. Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability. (PMID: 26340333) Twigg SR … Wilkie AO (American journal of human genetics 2015) 3 4 58
  4. Expression of ZIC family genes in meningiomas and other brain tumors. (PMID: 20199689) Aruga J … Yokota N (BMC cancer 2010) 3 22 58
  5. Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (PMID: 19010793) Baranzini SE … Oksenberg JR (Human molecular genetics 2009) 3 44 58

Products for ZIC1 Gene

Sources for ZIC1 Gene

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