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    ZIC1 Zic family member 1 [ Homo sapiens (human) ]

    Gene ID: 7545, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZIC1provided by HGNC
    Official Full Name
    Zic family member 1provided by HGNC
    Primary source
    HGNC:HGNC:12872
    See related
    Ensembl:ENSG00000152977 MIM:600470; AllianceGenome:HGNC:12872
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZIC; CRS6; BAIDCS; ZNF201
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 3.1), liver (RPKM 0.5) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See ZIC1 in Genome Data Viewer
    Location:
    3q24
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (147409365..147416719)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (150164618..150171972)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (147127152..147134506)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene leucine-rich repeat extensin-like protein 5 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:147094929-147095809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:147108264-147108780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:147108781-147109295 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:147111165-147111666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:147113516-147114253 Neighboring gene ZIC4 antisense RNA 1 Neighboring gene VISTA enhancer hs1043 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:147126759-147127339 Neighboring gene Zic family member 4 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:147129965-147130804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:147130805-147131644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20675 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:147138023-147138951 Neighboring gene uncharacterized LOC440982 Neighboring gene nucleophosmin 1 pseudogene 28

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. ZIC1 Dictates Osteogenesis Versus Adipogenesis in Human Mesenchymal Progenitor Cells Via a Hedgehog Dependent Mechanism. Thottappillil N, et al. Stem Cells, 2023 Sep 15. PMID 37317792, Free PMC Article
    2. Role of ZIC1 methylation in hepatocellular carcinoma and its clinical significance. Wang YY, et al. Tumour Biol, 2014 Aug. PMID 24782033
    3. Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers. Huang RL, et al. Epigenetics, 2013 Jun. PMID 23774800, Free PMC Article
    4. Zic1 Promoter Hypermethylation in Plasma DNA Is a Potential Biomarker for Gastric Cancer and Intraepithelial Neoplasia. Chen X, et al. PLoS One, 2015. PMID 26207911, Free PMC Article
    5. ZIC1 modulates cell-cycle distributions and cell migration through regulation of sonic hedgehog, PI(3)K and MAPK signaling pathways in gastric cancer. Zhong J, et al. BMC Cancer, 2012 Jul 16. PMID 22799764, Free PMC Article

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZIC1 Dictates Osteogenesis Versus Adipogenesis in Human Mesenchymal Progenitor Cells Via a Hedgehog Dependent Mechanism.
      Title: ZIC1 Dictates Osteogenesis Versus Adipogenesis in Human Mesenchymal Progenitor Cells Via a Hedgehog Dependent Mechanism.
    2. Common Variants Near ZIC1 and ZIC4 in Autopsy-Confirmed Multiple System Atrophy.
      Title: Common Variants Near ZIC1 and ZIC4 in Autopsy-Confirmed Multiple System Atrophy.
    3. Age-Related DNA Methylation in Normal Kidney Tissue Identifies Epigenetic Cancer Risk Susceptibility Loci in the ANKRD34B and ZIC1 Genes.
      Title: Age-Related DNA Methylation in Normal Kidney Tissue Identifies Epigenetic Cancer Risk Susceptibility Loci in the ANKRD34B and ZIC1 Genes.
    4. Mechanical-Stress-Related Epigenetic Regulation of ZIC1 Transcription Factor in the Etiology of Postmenopausal Osteoporosis.
      Title: Mechanical-Stress-Related Epigenetic Regulation of ZIC1 Transcription Factor in the Etiology of Postmenopausal Osteoporosis.
    5. Transcriptional expression of ZICs as an independent indicator of survival in gliomas.
      Title: Transcriptional expression of ZICs as an independent indicator of survival in gliomas.
    6. Roles and correlation of FOXA1 and ZIC1 in breast cancer.
      Title: Roles and correlation of FOXA1 and ZIC1 in breast cancer.
    7. LINC01419-mediated epigenetic silencing of ZIC1 promotes metastasis in hepatocellular carcinoma through the PI3K/Akt signaling pathway.
      Title: LINC01419-mediated epigenetic silencing of ZIC1 promotes metastasis in hepatocellular carcinoma through the PI3K/Akt signaling pathway.
    8. Zic1 suppresses gastric cancer metastasis by regulating Wnt/beta-catenin signaling and epithelial-mesenchymal transition.
      Title: Zic1 suppresses gastric cancer metastasis by regulating Wnt/β-catenin signaling and epithelial-mesenchymal transition.
    9. A single factor induces neuronal differentiation to suppress glioma cell growth.
      Title: A single factor induces neuronal differentiation to suppress glioma cell growth.
    10. this severe brain malformation indicates that premature closure of sutures can be independent of the abnormal brain development in subjects with pathogenic variants in ZIC1.
      Title: Mutated zinc finger protein of the cerebellum 1 leads to microcephaly, cortical malformation, callosal agenesis, cerebellar dysplasia, tethered cord and scoliosis.
    Submit: New GeneRIF Correction See all GeneRIFs (35)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Craniosynostosis 6
    MedGen: C4225269 OMIM: 616602 GeneReviews: Not available
    		Compare labs
    Structural brain anomalies with impaired intellectual development and craniosynostosis
    MedGen: C5231485 OMIM: 618736 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2021-07-19)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2021-07-19)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA-binding transcription factor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in brain development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in central nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hippocampus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in inner ear morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in maintenance of cell number IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in olfactory bulb development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in pattern specification process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of protein import into nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of smoothened signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spinal cord development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger protein ZIC 1
    Names
    Zic family member 1 (odd-paired homolog, Drosophila)
    Zinc finger protein of the cerebellum 1
    zinc finger protein 201

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_015886.1 RefSeqGene

      Range
      4972..12326
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003412.4 → NP_003403.2  zinc finger protein ZIC 1

      See identical proteins and their annotated locations for NP_003403.2

      Status: REVIEWED

      Source sequence(s)
      AC092959, BF920299
      Consensus CDS
      CCDS3136.1
      UniProtKB/Swiss-Prot
      Q15915, Q2M3N1
      Related
      ENSP00000282928.4, ENST00000282928.5
      Conserved Domains (3) summary
      COG5189
      Location:298 → 382
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:276 → 296
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18366
      Location:219 → 264
      zf_ZIC; Zic proteins zinc finger domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      147409365..147416719
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      150164618..150171972
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15915.2 GenPept UniProtKB/Swiss-Prot:Q15915

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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