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    ZIC3 Zic family member 3 [ Homo sapiens (human) ]

    Gene ID: 7547, updated on 5-Mar-2024

    Summary

    Official Symbol
    ZIC3provided by HGNC
    Official Full Name
    Zic family member 3provided by HGNC
    Primary source
    HGNC:HGNC:12874
    See related
    Ensembl:ENSG00000156925 MIM:300265; AllianceGenome:HGNC:12874
    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
    HTX; HTX1; ZNF203; VACTERLX
    Summary
    This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. This nuclear protein probably functions as a transcription factor in early stages of left-right body axis formation. Mutations in this gene cause X-linked visceral heterotaxy, which includes congenital heart disease and left-right axis defects in organs. [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
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    Genomic context

    See ZIC3 in Genome Data Viewer
    Location:
    Xq26.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (137566127..137577691)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (135876075..135887645)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (136648286..136659850)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Rac family small GTPase 1 pseudogene 4 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chrX:136631085-136631893 Neighboring gene long intergenic non-protein coding RNA 2931 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:136648687-136649272 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:136657825-136658375 Neighboring gene RNA, 7SL, cytoplasmic 325, pseudogene Neighboring gene zinc finger FYVE-type containing 9 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Heterotaxy, visceral, 1, X-linked
    MedGen: C1844020 OMIM: 306955 GeneReviews: Not available
    not available
    VACTERL association, X-linked, with or without hydrocephalus
    MedGen: C2931228 OMIM: 314390 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-12-02)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-12-02)

    ClinGen Genome Curation PagePubMed

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in atrial cardiac muscle tissue development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in axial mesoderm development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in central nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in central nervous system segmentation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cranial skeletal system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in determination of digestive tract left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in determination of left/right asymmetry in nervous system IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in determination of left/right symmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in determination of liver left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in determination of pancreatic left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in face development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in germ-line stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heart looping IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in hippocampus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in left/right axis specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in limb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lung development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mRNA transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural plate development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in olfactory bulb development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in outer ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in paraxial mesoderm development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in primitive streak formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in skeletal system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    zinc finger protein ZIC 3
    Names
    Zic family member 3 (odd-paired homolog, Drosophila)
    heterotaxy 1
    zinc finger protein 203
    zinc finger protein of the cerebellum 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008115.2 RefSeqGene

      Range
      5001..10976
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001330661.1NP_001317590.1  zinc finger protein ZIC 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as ZIC3-B) uses an alternate 3'-terminal exon, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL035443
      Consensus CDS
      CCDS83494.1
      UniProtKB/Swiss-Prot
      O60481
      Related
      ENSP00000359638.3, ENST00000370606.3
    2. NM_003413.4NP_003404.1  zinc finger protein ZIC 3 isoform 1

      See identical proteins and their annotated locations for NP_003404.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as ZIC3-A) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL035443
      Consensus CDS
      CCDS14663.1
      UniProtKB/Swiss-Prot
      B2CNW4, O60481, Q14DE5, Q5JY75
      Related
      ENSP00000287538.5, ENST00000287538.10
      Conserved Domains (2) summary
      COG5189
      Location:324408
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:302322
      ZF_C2H2; C2H2 Zn finger [structural motif]

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      137566127..137577691
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      135876075..135887645
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)