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

Gene ID: 7546, updated on 10-Dec-2019

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
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

Genomic context

See ZIC2 in Genome Data Viewer
Location:
13q32.3
Exon count:
3
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (99981784..99986765)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (100634026..100639019)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene citrate lyase beta like Neighboring gene uncharacterized LOC101927437 Neighboring gene Zic family member 2 polyalanine repeat instability region 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
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-07-06)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-06)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
    Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
brain development TAS
Traceable Author Statement
more info
PubMed 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
visual perception ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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)

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
    UniProtKB/TrEMBL
    A0A024RDY6
    Related
    ENSP00000365514.3, ENST00000376335.8
    Conserved Domains (3) summary
    COG5048
    Location:243436
    COG5048; FOG: Zn-finger [General function prediction only]
    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]

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

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