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

Gene ID: 7545, updated on 5-Mar-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
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Genomic context

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Location:
3q24
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (147409365..147416719)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (150164618..150171972)
105.20220307 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
  • 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. Mechanical-Stress-Related Epigenetic Regulation of ZIC1 Transcription Factor in the Etiology of Postmenopausal Osteoporosis. Datta HK, et al. Int J Mol Sci, 2022 Mar 9. PMID 35328378, Free PMC Article
  2. Zic1 suppresses gastric cancer metastasis by regulating Wnt/β-catenin signaling and epithelial-mesenchymal transition. Ge Q, et al. FASEB J, 2020 Feb. PMID 31909528
  3. Mutated zinc finger protein of the cerebellum 1 leads to microcephaly, cortical malformation, callosal agenesis, cerebellar dysplasia, tethered cord and scoliosis. Vandervore LV, et al. Eur J Med Genet, 2018 Dec. PMID 30391508
  4. A single factor induces neuronal differentiation to suppress glioma cell growth. Fu JQ, et al. CNS Neurosci Ther, 2019 Apr. PMID 30264483, Free PMC Article
  5. ZIC1 Function in Normal Cerebellar Development and Human Developmental Pathology. Aruga J, et al. Adv Exp Med Biol, 2018. PMID 29442326

See all (52) 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_2023_10

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

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