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    ZIC2 Zic family member 2 [ Homo sapiens (human) ]

    Gene ID: 7546, updated on 5-May-2024

    Summary

    Official Symbol
    ZIC2provided by HGNC
    Official Full Name
    Zic family member 2provided by HGNC
    Primary source
    HGNC:HGNC:12873
    See related
    Ensembl:ENSG00000043355 MIM:603073; AllianceGenome:HGNC:12873
    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
    HPE5
    Summary
    This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. This protein functions as a transcriptional repressor and may regulate tissue specific expression of dopamine receptor D1. Expansion of an alanine repeat in the C-terminus of the encoded protein and other mutations in this gene cause holoprosencephaly type 5. Holoprosencephaly is the most common structural anomaly of the human brain. A polyhistidine tract polymorphism in this gene may be associated with increased risk of neural tube defects. This gene is closely linked to a gene encoding zinc finger protein of the cerebellum 5, a related family member on chromosome 13. [provided by RefSeq, Jul 2016]
    Expression
    Biased expression in brain (RPKM 3.1) and testis (RPKM 0.7) See more
    Orthologs
    NEW
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    Genomic context

    See ZIC2 in Genome Data Viewer
    Location:
    13q32.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (99981784..99986765)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (99192694..99197676)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (100634038..100639019)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene citramalyl-CoA lyase Neighboring gene CLYBL antisense RNA 3 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100461465-100461966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100461967-100462466 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:100470112-100470282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100485830-100486582 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:100506615-100507814 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100544348-100544902 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100544903-100545456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100545457-100546010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100547191-100547692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100547693-100548192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100552816-100553392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100556702-100557202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100565623-100566124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100566125-100566624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100582975-100583475 Neighboring gene Sharpr-MPRA regulatory region 10052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100608499-100609474 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100609475-100610449 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100626468-100627010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100627011-100627551 Neighboring gene OCT4 hESC enhancer GRCh37_chr13:100631077-100631586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5475 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:100635796-100636995 Neighboring gene Zic family member 2 polyalanine repeat instability region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100642562-100643511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100649774-100650719 Neighboring gene Zic family member 5 Neighboring gene long intergenic non-protein coding RNA 554 Neighboring gene NADH:ubiquinone oxidoreductase subunit A12 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
    Holoprosencephaly 5
    MedGen: C1864827 OMIM: 609637 GeneReviews: Holoprosencephaly Overview
    not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2022-08-24)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2022-08-24)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia.
    EBI GWAS Catalog
    Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
    EBI GWAS Catalog
    Genome-wide meta-analysis of myopia and hyperopia provides evidence for replication of 11 Loci.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 chromatin DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in brain development TAS
    Traceable Author Statement
    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 negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of DNA-binding transcription factor activity 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 regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in visual perception ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear body IDA
    Inferred from Direct Assay
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    zinc finger protein ZIC 2
    Names
    Zic family member 2 (odd-paired homolog, Drosophila)
    Zinc finger protein of the cerebellum 2

    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_007085.3 RefSeqGene

      Range
      5029..10010
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1157

    mRNA and Protein(s)

    1. NM_007129.5NP_009060.2  zinc finger protein ZIC 2

      See identical proteins and their annotated locations for NP_009060.2

      Status: REVIEWED

      Source sequence(s)
      AA491603, AF193855, AL355338
      Consensus CDS
      CCDS9495.1
      UniProtKB/Swiss-Prot
      O95409, Q5VYA9, Q9H309
      Related
      ENSP00000365514.3, ENST00000376335.8
      Conserved Domains (3) summary
      COG5189
      Location:329413
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:307327
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18366
      Location:250295
      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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      99981784..99986765
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      99192694..99197676
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)