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ZFHX3 zinc finger homeobox 3 [ Homo sapiens (human) ]

Gene ID: 463, updated on 12-Oct-2019

Summary

Official Symbol
ZFHX3provided by HGNC
Official Full Name
zinc finger homeobox 3provided by HGNC
Primary source
HGNC:HGNC:777
See related
Ensembl:ENSG00000140836 MIM:104155
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
ATBT; ATBF1; ZFH-3; ZNF927; C16orf47
Summary
This gene encodes a transcription factor with multiple homeodomains and zinc finger motifs, and regulates myogenic and neuronal differentiation. The encoded protein suppresses expression of the alpha-fetoprotein gene by binding to an AT-rich enhancer motif. The protein has also been shown to negatively regulate c-Myb, and transactivate the cell cycle inhibitor cyclin-dependent kinase inhibitor 1A (also known as p21CIP1). This gene is reported to function as a tumor suppressor in several cancers, and sequence variants of this gene are also associated with atrial fibrillation. Multiple transcript variants expressed from alternate promoters and encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
Expression
Ubiquitous expression in thyroid (RPKM 3.0), prostate (RPKM 2.4) and 25 other tissues See more
Orthologs

Genomic context

See ZFHX3 in Genome Data Viewer
Location:
16q22.2-q22.3
Exon count:
22
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (72782885..73891931, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (72816784..73092534, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984814 Neighboring gene VISTA enhancer hs20 Neighboring gene uncharacterized LOC101927978 Neighboring gene keratin 18 pseudogene 18 Neighboring gene RNA, U7 small nuclear 71 pseudogene Neighboring gene Sharpr-MPRA regulatory region 11593 Neighboring gene VISTA enhancer hs16 Neighboring gene HCCAT5-C16orf47 intergenic CAGE-defined high expression enhancer Neighboring gene hepatocellular carcinoma associated transcript 5 Neighboring gene VISTA enhancer hs1724 Neighboring gene long intergenic non-protein coding RNA 1568 Neighboring gene tRNA-Lys (anticodon TTT) 1-1 Neighboring gene Sharpr-MPRA regulatory region 9376 Neighboring gene uncharacterized LOC102723876 Neighboring gene VISTA enhancer hs1612 Neighboring gene uncharacterized LOC105371342 Neighboring gene uncharacterized LOC107984856 Neighboring gene ribosomal protein SA pseudogene 56

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
Malignant tumor of prostate
MedGen: C0376358 OMIM: 176807 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study identifies novel and functionally related susceptibility Loci for Kawasaki disease.
NHGRI GWA Catalog
A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke.
NHGRI GWA Catalog
Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE collaboration): a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
NHGRI GWA Catalog
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
NHGRI GWA Catalog
Meta-analysis identifies six new susceptibility loci for atrial fibrillation.
NHGRI GWA Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
NHGRI GWA Catalog
Variants in ZFHX3 are associated with atrial fibrillation in individuals of European ancestry.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ26184

Gene Ontology Provided by GOA

Process Evidence Code Pubs
brain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell cycle arrest IEA
Inferred from Electronic Annotation
more info
 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
muscle organ development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of locomotor rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
response to transforming growth factor beta IDA
Inferred from Direct Assay
more info
PubMed 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus TAS
Traceable Author Statement
more info
PubMed 
transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
zinc finger homeobox protein 3
Names
AT motif-binding factor 1
AT-binding transcription factor 1
alpha-fetoprotein enhancer binding protein
zinc finger homeodomain protein 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_013211.2 RefSeqGene

    Range
    848804..1114047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001164766.2NP_001158238.1  zinc finger homeobox protein 3 isoform B

    Status: REVIEWED

    Description
    Transcript Variant: This variant (B) represents use of an alternate promoter and 5' UTR, lacks an alternate coding exon, and uses a downstream start codon, compared to variant A. The resulting isoform (B) has a shorter N-terminus, compared to isoform A.
    Source sequence(s)
    AC004943, AC116667, D10250, L32832
    Consensus CDS
    CCDS54035.1
    UniProtKB/Swiss-Prot
    Q15911
    Related
    ENSP00000438926.3, ENST00000397992.5
    Conserved Domains (5) summary
    smart00389
    Location:12311287
    HOX; Homeodomain
    COG5576
    Location:16801824
    COG5576; Homeodomain-containing transcription factor [Transcription]
    sd00017
    Location:633657
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:489509
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:17311783
    Homeobox; Homeobox domain
  2. NM_006885.4NP_008816.3  zinc finger homeobox protein 3 isoform A

    See identical proteins and their annotated locations for NP_008816.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (A) represents the longer transcript and encodes the longer isoform (A). Expression of this variant is activated during neuronal differentiation.
    Source sequence(s)
    AC002044, AC004943, AC132068, BC029653
    Consensus CDS
    CCDS10908.1
    UniProtKB/Swiss-Prot
    Q15911
    UniProtKB/TrEMBL
    Q8N2Y6
    Related
    ENSP00000268489.5, ENST00000268489.10
    Conserved Domains (5) summary
    smart00389
    Location:21452201
    HOX; Homeodomain
    COG5576
    Location:25942738
    COG5576; Homeodomain-containing transcription factor [Transcription]
    sd00017
    Location:15471571
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:14031423
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:26452697
    Homeobox; Homeobox domain

RNA

  1. NR_163978.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC116667
    Related
    ENST00000358463.2

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_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    72782885..73891931 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255957.4XP_005256014.1  zinc finger homeobox protein 3 isoform X1

    Conserved Domains (5) summary
    smart00389
    Location:21442200
    HOX; Homeodomain
    COG5576
    Location:25932737
    COG5576; Homeodomain-containing transcription factor [Transcription]
    sd00017
    Location:15461570
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:14021422
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:26442696
    Homeobox; Homeobox domain
  2. XM_024450291.1XP_024306059.1  zinc finger homeobox protein 3 isoform X3

    Conserved Domains (6) summary
    smart00389
    Location:12611317
    HOX; Homeodomain
    sd00017
    Location:663687
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:519539
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:17611813
    Homeobox; Homeobox domain
    cl25496
    Location:22202307
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl27820
    Location:17101854
    Abdominal-A; Homeobox protein
  3. XM_017023251.2XP_016878740.1  zinc finger homeobox protein 3 isoform X2

  4. XM_024450275.1XP_024306043.1  zinc finger homeobox protein 3 isoform X1

  5. XM_024450276.1XP_024306044.1  zinc finger homeobox protein 3 isoform X1

  6. XM_017023229.1XP_016878718.1  zinc finger homeobox protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZP98
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