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Aliases for ZIC4 Gene

Aliases for ZIC4 Gene

  • Zic Family Member 4 2 3 5
  • Zinc Finger Protein Of The Cerebellum 4 2 4

External Ids for ZIC4 Gene

Previous GeneCards Identifiers for ZIC4 Gene

  • GC03M143947
  • GC03M147990
  • GC03M148386
  • GC03M148426
  • GC03M148587
  • GC03M147103
  • GC03M144480

Summaries for ZIC4 Gene

Entrez Gene Summary for ZIC4 Gene

  • This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. Members of this family are important during development, and have been associated with X-linked visceral heterotaxy and holoprosencephaly type 5. This gene is closely linked to the gene encoding zinc finger protein of the cerebellum 1, a related family member on chromosome 3. Heterozygous deletion of these linked genes is involved in Dandy-Walker malformation, which is a congenital cerebellar malformation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Dec 2009]

GeneCards Summary for ZIC4 Gene

ZIC4 (Zic Family Member 4) is a Protein Coding gene. Diseases associated with ZIC4 include Isolated Dandy-Walker Malformation Without Hydrocephalus and Isolated Dandy-Walker Malformation With Hydrocephalus. An important paralog of this gene is ZIC1.

UniProtKB/Swiss-Prot for ZIC4 Gene

  • Binds to DNA.

Additional gene information for ZIC4 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZIC4 Gene

Genomics for ZIC4 Gene

GeneHancer (GH) Regulatory Elements for ZIC4 Gene

Promoters and enhancers for ZIC4 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
GH03I147406 Promoter/Enhancer 0.9 EPDnew dbSUPER 550.8 +0.7 695 0.1 SUZ12 EZH2 ZIC4 ZIC1
GH03I147404 Promoter/Enhancer 0.8 EPDnew dbSUPER 550.8 +2.6 2559 0.1 EZH2 ZIC4 ZIC1
GH03I147419 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 20.2 -11.8 -11839 0.2 ZNF639 MEIS2 MXI1 USF1 L3MBTL2 ZBTB2 SUZ12 BHLHE40 NRF1 MAX ZIC1 ZIC4 ZIC4-AS1 ENSG00000243620 LOC440982
GH03I146975 Enhancer 0.7 UCNEbase FANTOM5 17.5 +431.9 431867 0.3 ZIC4 ZIC1 GC03M146997 RNU6-505P LINC02010 ENSG00000243620
GH03I147424 Enhancer 0.7 FANTOM5 dbSUPER 11.5 -17.0 -17045 0.2 CTBP2 EZH2 ZIC1 ZIC4-AS1 ZIC4 ENSG00000243620 LOC440982 NPM1P28
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZIC4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZIC4 gene promoter:

Genomic Locations for ZIC4 Gene

Genomic Locations for ZIC4 Gene
21,431 bases
Minus strand

Genomic View for ZIC4 Gene

Genes around ZIC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZIC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZIC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZIC4 Gene

Proteins for ZIC4 Gene

  • Protein details for ZIC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger protein ZIC 4
    Protein Accession:
    Secondary Accessions:
    • A0AVA2
    • B2RMQ8
    • B4DF89
    • B7Z2L2
    • C9J7D5
    • J3KQG1
    • Q4G157
    • Q9BZ94

    Protein attributes for ZIC4 Gene

    334 amino acids
    Molecular mass:
    36567 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH29507.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence starting in position 229.; Evidence={ECO:0000305}; Sequence=AAK06845.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for ZIC4 Gene


neXtProt entry for ZIC4 Gene

Post-translational modifications for ZIC4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ZIC4 Gene

Domains & Families for ZIC4 Gene

Gene Families for ZIC4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins
  • Transcription factors

Protein Domains for ZIC4 Gene


Suggested Antigen Peptide Sequences for ZIC4 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the GLI C2H2-type zinc-finger protein family.
  • Belongs to the GLI C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with ZIC4: view

Function for ZIC4 Gene

Molecular function for ZIC4 Gene

UniProtKB/Swiss-Prot Function:
Binds to DNA.

Phenotypes From GWAS Catalog for ZIC4 Gene

Gene Ontology (GO) - Molecular Function for ZIC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding ISS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZIC4: view
genes like me logo Genes that share phenotypes with ZIC4: view

Animal Models for ZIC4 Gene

MGI Knock Outs for ZIC4:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ZIC4 Gene

Localization for ZIC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZIC4 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 ZIC4 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZIC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
genes like me logo Genes that share ontologies with ZIC4: view

Pathways & Interactions for ZIC4 Gene

No Data Available

Interacting Proteins for ZIC4 Gene

Gene Ontology (GO) - Biological Process for ZIC4 Gene


No data available for Pathways by source and SIGNOR curated interactions for ZIC4 Gene

Drugs & Compounds for ZIC4 Gene

No Compound Related Data Available

Transcripts for ZIC4 Gene

Unigene Clusters for ZIC4 Gene

Zic family member 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZIC4 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d · 7e ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c · 10d ^ 11
SP1: - - -
SP2: - - -
SP3: - - - -
SP4: - - - - - - - - - - - - -
SP5: - - -
SP6: -
SP9: -

Relevant External Links for ZIC4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZIC4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZIC4 Gene

mRNA differential expression in normal tissues according to GTEx for ZIC4 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x24.1) and Brain - Cerebellum (x21.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ZIC4 Gene

Protein tissue co-expression partners for ZIC4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZIC4 Gene:


SOURCE GeneReport for Unigene cluster for ZIC4 Gene:


Evidence on tissue expression from TISSUES for ZIC4 Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with ZIC4: view

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZIC4 Gene

Orthologs for ZIC4 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZIC4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZIC4 33 34
  • 99.74 (n)
(Bos Taurus)
Mammalia ZIC4 33 34
  • 92.62 (n)
(Canis familiaris)
Mammalia ZIC4 33 34
  • 92.02 (n)
(Mus musculus)
Mammalia Zic4 33 16 34
  • 87.03 (n)
(Ornithorhynchus anatinus)
Mammalia ZIC4 34
  • 75 (a)
(Monodelphis domestica)
Mammalia ZIC4 34
  • 73 (a)
(Gallus gallus)
Aves ZIC4 33 34
  • 74.84 (n)
(Anolis carolinensis)
Reptilia ZIC4 34
  • 62 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia zic4 33
  • 73.19 (n)
(Danio rerio)
Actinopterygii zic4 33 34
  • 73.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta opa 34
  • 28 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
Species where no ortholog for ZIC4 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 ZIC4 Gene

Gene Tree for ZIC4 (if available)
Gene Tree for ZIC4 (if available)

Paralogs for ZIC4 Gene

Paralogs for ZIC4 Gene

genes like me logo Genes that share paralogs with ZIC4: view

Variants for ZIC4 Gene

Sequence variations from dbSNP and Humsavar for ZIC4 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs17509456 conflicting-interpretations-of-pathogenicity, not specified 147,390,969(-) C/A/G coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs6766244 benign, not specified 147,403,964(-) C/T coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, synonymous_variant
rs1000113616 -- 147,393,642(-) T/C downstream_transcript_variant, genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000203267 -- 147,394,113(-) T/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000269588 -- 147,398,935(-) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZIC4 Gene

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

Variation tolerance for ZIC4 Gene

Residual Variation Intolerance Score: 83.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.43; 42.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZIC4 Gene

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 ZIC4 Gene

Disorders for ZIC4 Gene

MalaCards: The human disease database

(4) MalaCards diseases for ZIC4 Gene - From: Orphanet and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search ZIC4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ZIC4

genes like me logo Genes that share disorders with ZIC4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ZIC4 Gene

Publications for ZIC4 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. Comparative analysis of a 229-kb medaka genomic region, containing the zic1 and zic4 genes, with Fugu, human, and mouse. (PMID: 15177559) Ohtsuka M … Kimura M (Genomics 2004) 3 22 58
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58
  5. Genome-wide analysis of CpG island methylation in bladder cancer identified TBX2, TBX3, GATA2, and ZIC4 as pTa-specific prognostic markers. (PMID: 22284968) Kandimalla R … Zwarthoff EC (European urology 2012) 3 58

Products for ZIC4 Gene

Sources for ZIC4 Gene

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