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 o... See more...

Aliases for ZIC4 Gene

Aliases for ZIC4 Gene

  • Zic Family Member 4 2 3 5
  • Zinc Finger Protein Of The Cerebellum 4 2 3 4
  • Zinc Finger Protein ZIC 4 3 4
  • Zinc Family Member 4 Protein HZIC4 3

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 Summary for ZIC4 Gene

Additional gene information for ZIC4 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J147407 Promoter/Enhancer 2.2 VISTA EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 -3.3 -3325 7.2 EP300 USF1 ZBTB26 EZH2 SMC3 SP2 MXI1 YY1 TCF12 CBX8 ZIC1 ZIC4 lnc-ZIC4-4 ENSG00000243620
GH03J147406 Promoter/Enhancer 0.9 EPDnew Ensembl dbSUPER 500.7 +0.6 600 0.2 CBX8 RNF2 SUZ12 EZH2 ZIC4 lnc-PLSCR5-2 ZIC1
GH03J147408 Promoter/Enhancer 0.7 EPDnew dbSUPER 500.7 +1.4 1400 0.1 RNF2 SUZ12 EZH2 ZIC4 lnc-PLSCR5-2 ZIC1
GH03J147419 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 20.2 -11.8 -11839 0.2 NRF1 MYC USF1 HDAC2 EZH2 SMC3 MXI1 YY1 E2F6 POU2F2 HSALNG0029661 ZIC1 ZIC4 ZIC4-AS1 ENSG00000243620 LOC440982
GH03J146975 Enhancer 0.5 UCNEbase FANTOM5 17.5 +431.9 431867 0.3 ZIC4 ZIC1 piR-40476-047 piR-41876-005 ENSG00000243620
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZIC4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ZIC4

Top Transcription factor binding sites by QIAGEN in the ZIC4 gene promoter:
  • IRF-7A
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • Pbx1a
  • SRY
  • USF-1
  • USF-1:USF-2

Genomic Locations for ZIC4 Gene

Genomic Locations for ZIC4 Gene
chr3:147,386,046-147,407,476
(GRCh38/hg38)
Size:
21,431 bases
Orientation:
Minus strand
chr3:147,103,833-147,124,647
(GRCh37/hg19)
Size:
20,815 bases
Orientation:
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:
    Q8N9L1-ZIC4_HUMAN
    Recommended name:
    Zinc finger protein ZIC 4
    Protein Accession:
    Q8N9L1
    Secondary Accessions:
    • A0AVA2
    • B2RMQ8
    • B4DF89
    • B7Z2L2
    • C9J7D5
    • J3KQG1
    • Q4G157
    • Q9BZ94

    Protein attributes for ZIC4 Gene

    Size:
    334 amino acids
    Molecular mass:
    36567 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • [Isoform 2]: May be due to an intron retention.
    SequenceCaution:
    • 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=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for ZIC4 Gene

    UniProtKB/Swiss-Prot:

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

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

Protein Domains for ZIC4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ZIC4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ58759, highly similar to Zinc finger protein ZIC 4 (B7Z2L2_HUMAN)
  • Zinc finger protein of the cerebellum 4 (ZIC4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N9L1

UniProtKB/Swiss-Prot:

ZIC4_HUMAN :
  • Belongs to the GLI C2H2-type zinc-finger protein family.
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:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific IBA 21873635
GO:0003676 nucleic acid binding IEA --
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:

Animal Model Products

CRISPR Products

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

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 ZIC4 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for ZIC4 Gene

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

Pathways & Interactions for ZIC4 Gene

PathCards logo

SuperPathways for ZIC4 Gene

No Data Available

Interacting Proteins for ZIC4 Gene

;

Gene Ontology (GO) - Biological Process for ZIC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007417 central nervous system development IBA 21873635
genes like me logo Genes that share ontologies with ZIC4: view

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

mRNA/cDNA for ZIC4 Gene

4 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
17 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

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: -
SP7:
SP8:
SP9: -

Relevant External Links for ZIC4 Gene

GeneLoc Exon Structure for
ZIC4

Expression for ZIC4 Gene

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



Protein tissue co-expression partners for ZIC4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ZIC4

SOURCE GeneReport for Unigene cluster for ZIC4 Gene:

Hs.415766

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
chimpanzee
(Pan troglodytes)
Mammalia ZIC4 31 30
  • 99.74 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ZIC4 31 30
  • 92.62 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ZIC4 31 30
  • 92.02 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Zic4 17 31 30
  • 87.03 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ZIC4 31
  • 75 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ZIC4 31
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves ZIC4 31 30
  • 74.84 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ZIC4 31
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia zic4 30
  • 73.19 (n)
zebrafish
(Danio rerio)
Actinopterygii zic4 31 30
  • 73.21 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta opa 31
  • 28 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 34 (a)
ManyToMany
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

ENSEMBL:
Gene Tree for ZIC4 (if available)
TreeFam:
Gene Tree for ZIC4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZIC4: view image

Paralogs for ZIC4 Gene

Paralogs for ZIC4 Gene

(19) SIMAP similar genes for ZIC4 Gene using alignment to 4 proteins:

  • ZIC4_HUMAN
  • C9J6T3_HUMAN
  • C9JD04_HUMAN
  • C9JZU7_HUMAN
genes like me logo Genes that share paralogs with ZIC4: view

Variants for ZIC4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ZIC4 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
729089 Benign: not provided 147,391,095(-) C/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
731775 Likely Benign: not provided 147,404,093(-) C/T SYNONYMOUS_VARIANT,INTRON_VARIANT
778289 Benign: not provided 147,390,970(-) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs17509456 Benign: not specified 147,390,969(-) C/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
rs6766244 Benign: not specified 147,403,964(-) C/T SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for ZIC4 Gene

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
ZIC4

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

(10) MalaCards diseases for ZIC4 Gene - From: Orphanet, DISEASES, 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

No publications were found for ZIC4 Gene.

Products for ZIC4 Gene

Sources for ZIC4 Gene