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

Gene ID: 7547, updated on 28-Oct-2019

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
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

Genomic context

See ZIC3 in Genome Data Viewer
Location:
Xq26.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (137566127..137577691)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (136648346..136654259)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs755 Neighboring gene Rac family small GTPase 1 pseudogene 4 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, X-linked
MedGen: C1844020 OMIM: 306955 GeneReviews: Not available
Compare labs
VACTERL association with hydrocephaly, X-linked
MedGen: C1839115 OMIM: 314390 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

ClinGen Genome Curation PagePubMed

Pathways from BioSystems

  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • 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...
  • POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation, organism-specific biosystem (from REACTOME)
    POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation, organism-specific biosystemPOU5F1 (OCT4), SOX2, and NANOG bind elements in the promoters of target genes. The target genes of each transcription factor overlap extensively: POU5F1, SOX2, and NANOG co-occupy at least 353 genes ...
  • Signaling pathways regulating pluripotency of stem cells, organism-specific biosystem (from KEGG)
    Signaling pathways regulating pluripotency of stem cells, organism-specific biosystemPluripotent stem cells (PSCs) are basic cells with an indefinite self-renewal capacity and the potential to generate all the cell types of the three germinal layers. The types of PSCs known to date i...
  • Signaling pathways regulating pluripotency of stem cells, conserved biosystem (from KEGG)
    Signaling pathways regulating pluripotency of stem cells, conserved biosystemPluripotent stem cells (PSCs) are basic cells with an indefinite self-renewal capacity and the potential to generate all the cell types of the three germinal layers. The types of PSCs known to date i...
  • Transcriptional regulation of pluripotent stem cells, organism-specific biosystem (from REACTOME)
    Transcriptional regulation of pluripotent stem cells, organism-specific biosystemPluripotent stem cells are undifferentiated cells posessing an abbreviated cell cycle (reviewed in Stein et al. 2012), a characteristic profile of gene expression (Rao et al. 2004, Kim et al. 2006, P...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
determination of digestive tract left/right asymmetry IMP
Inferred from Mutant Phenotype
more info
PubMed 
determination of left/right asymmetry in nervous system IEA
Inferred from Electronic Annotation
more info
 
determination of left/right symmetry IMP
Inferred from Mutant Phenotype
more info
PubMed 
determination of liver left/right asymmetry IMP
Inferred from Mutant Phenotype
more info
PubMed 
determination of pancreatic left/right asymmetry IMP
Inferred from Mutant Phenotype
more info
PubMed 
heart looping IMP
Inferred from Mutant Phenotype
more info
PubMed 
lung development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
somatic stem cell population maintenance TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
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 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)

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
    O60481
    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: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

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