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ZIC4 Zic family member 4 [ Homo sapiens (human) ]

Gene ID: 84107, updated on 12-Oct-2019

Summary

Official Symbol
ZIC4provided by HGNC
Official Full Name
Zic family member 4provided by HGNC
Primary source
HGNC:HGNC:20393
See related
Ensembl:ENSG00000174963 MIM:608948
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
Summary
This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. Members of this family are important during development, and have been associated with X-linked visceral heterotaxy and holoprosencephaly type 5. This gene is closely linked to the gene encoding zinc finger protein of the cerebellum 1, a related family member on chromosome 3. Heterozygous deletion of these linked genes is involved in Dandy-Walker malformation, which is a congenital cerebellar malformation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Dec 2009]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See ZIC4 in Genome Data Viewer
Location:
3q24
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (147386048..147407476, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (147103835..147124596, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21 pseudogene 71 Neighboring gene VISTA enhancer hs213 Neighboring gene VISTA enhancer hs1043 Neighboring gene uncharacterized LOC440982 Neighboring gene Zic family member 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

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-03-15)

ClinGen Genome Curation Page
Haploinsufficency

Some evidence for dosage pathogenicity (Last evaluated (2012-03-15)

ClinGen Genome Curation PagePubMed

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ42609, FLJ45833

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, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
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 4
Names
zinc family member 4 protein HZIC4
zinc finger protein of the cerebellum 4

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_009242.1 RefSeqGene

    Range
    4812..25573
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001168378.1NP_001161850.1  zinc finger protein ZIC 4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001161850.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK124600, AK294831, DA066220
    Consensus CDS
    CCDS54652.1
    UniProtKB/Swiss-Prot
    Q8N9L1
    Related
    ENSP00000435509.2, ENST00000525172.6
    Conserved Domains (4) summary
    COG5048
    Location:192338
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:228248
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:314338
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:270297
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001168379.1NP_001161851.1  zinc finger protein ZIC 4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1, resulting in an isoform (2) with a distinct and shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK124600, AK293981, DA066220
    Consensus CDS
    CCDS54653.1
    UniProtKB/Swiss-Prot
    Q8N9L1
    Related
    ENSP00000397695.3, ENST00000425731.7
    Conserved Domains (4) summary
    COG5048
    Location:180326
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:216236
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:302326
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:258285
    zf-H2C2_2; Zinc-finger double domain
  3. NM_001243256.1NP_001230185.1  zinc finger protein ZIC 4 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and has multiple differences in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AK124600, DA102161, DA218617, DA759114
    Consensus CDS
    CCDS58857.1
    UniProtKB/Swiss-Prot
    Q8N9L1
    Related
    ENSP00000418277.1, ENST00000491672.5
    Conserved Domains (2) summary
    COG5189
    Location:2080
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:3052
    ZF_C2H2; C2H2 Zn finger [structural motif]
  4. NM_032153.5NP_115529.2  zinc finger protein ZIC 4 isoform 3

    See identical proteins and their annotated locations for NP_115529.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream, in-frame start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK056262, AK124600, DA102161
    Consensus CDS
    CCDS43160.1
    UniProtKB/Swiss-Prot
    Q8N9L1
    Related
    ENSP00000372553.3, ENST00000383075.7
    Conserved Domains (4) summary
    COG5048
    Location:142288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:264288
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:220247
    zf-H2C2_2; Zinc-finger double domain

RNA

  1. NR_033118.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks three 5' exons but includes an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AK124600, AK127733, DA106797, DA121447, DA314072
    Related
    ENST00000472749.6
  2. NR_033119.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks three 5' exons but includes an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AK124600, AK127733, DA121447, DA314072, DA416382
  3. NR_040762.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks three 5' exons but includes an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AK124600, DA121447, DA411998

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_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    147386048..147407476 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007314.2XP_016862803.1  zinc finger protein ZIC 4 isoform X1

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