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

    Gene ID: 463, updated on 8-Jul-2024

    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; AllianceGenome:HGNC:777
    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; SCA4; ATBF1; ATFB8; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ZFHX3 in Genome Data Viewer
    Location:
    16q22.2-q22.3
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (72782885..73891930, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (78600697..79709756, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (72816784..73925829, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2952 Neighboring gene VISTA enhancer hs20 Neighboring gene ZFHX3 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:72756067-72756616 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:72756617-72757164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:72769685-72770266 Neighboring gene RNA, U7 small nuclear 90 pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44255 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:72804631-72805830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:72822417-72823032 Neighboring gene keratin 18 pseudogene 18 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72879311-72879810 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7689 Neighboring gene uncharacterized LOC124903715 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:72910943-72912142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72912157-72912658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72923795-72924295 Neighboring gene RNA, U7 small nuclear 71 pseudogene Neighboring gene Sharpr-MPRA regulatory region 14271 Neighboring gene Sharpr-MPRA regulatory region 11593 Neighboring gene VISTA enhancer hs16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72995175-72995675 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73049174-73049674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11101 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73066446-73067008 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73069350-73070204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73070205-73071057 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73074111-73074623 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73078457-73078957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73081321-73081856 Neighboring gene uncharacterized LOC124903719 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73082393-73082928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73089102-73089614 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73087036-73087536 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73087537-73088037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7694 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73091454-73092186 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73098351-73098972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73126852-73127352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73127353-73127853 Neighboring gene HCCAT5-C16orf47 intergenic CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11103 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:73186584-73187107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73190308-73190808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73190809-73191309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73204295-73204796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73204797-73205296 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73205367-73206216 Neighboring gene NANOG hESC enhancer GRCh37_chr16:73230564-73231065 Neighboring gene hepatocellular carcinoma associated transcript 5 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:73266082-73267281 Neighboring gene uncharacterized LOC124903716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11105 Neighboring gene VISTA enhancer hs1724 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:73368016-73368182 Neighboring gene lncRNA oncogene in head and neck cancer 2 Neighboring gene tRNA-Lys (anticodon TTT) 1-1 Neighboring gene uncharacterized LOC124903717 Neighboring gene Sharpr-MPRA regulatory region 9376 Neighboring gene uncharacterized LOC102723876 Neighboring gene VISTA enhancer hs1612 Neighboring gene uncharacterized LOC105371342 Neighboring gene Sharpr-MPRA regulatory region 15378 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:73951504-73952703 Neighboring gene uncharacterized LOC124903721 Neighboring gene uncharacterized LOC107984856 Neighboring gene Sharpr-MPRA regulatory region 11065 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
    Atrial fibrillation, familial, 8
    MedGen: C2751607 OMIM: 613055 GeneReviews: Not available
    Compare labs
    Malignant tumor of prostate
    MedGen: C0376358 GeneReviews: Not available
    Compare labs
    Spinocerebellar ataxia type 4
    MedGen: C0752122 OMIM: 600223 GeneReviews: Hereditary Ataxia Overview
    Compare labs

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ26184

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus TAS
    Traceable Author Statement
    more info
    PubMed 
    part_of transcription regulator 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)

    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_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_001386735.1NP_001373664.1  zinc finger homeobox protein 3 isoform A

      Status: REVIEWED

      Source sequence(s)
      AC004943, AC009033, AC009104, AC092128, AC092344, AC116667, AC132068, AC137520
      Consensus CDS
      CCDS10908.1
      UniProtKB/Swiss-Prot
      D3DWS8, O15101, Q13719, Q15911, Q6ZP98
      Related
      ENSP00000493252.1, ENST00000641206.2
      Conserved Domains (6) 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]
      pfam05109
      Location:31043191
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam00046
      Location:22452299
      Homeobox; Homeobox domain
    3. 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) encodes the longer isoform (A). Variants A and D both encode the same 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
      D3DWS8, O15101, Q13719, Q15911, Q6ZP98
      Related
      ENSP00000268489.5, ENST00000268489.10
      Conserved Domains (6) 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]
      pfam05109
      Location:31043191
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam00046
      Location:22452299
      Homeobox; Homeobox domain

    RNA

    1. NR_163978.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC116667
      Related
      ENST00000358463.2

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      72782885..73891930 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434166.1XP_047290122.1  zinc finger homeobox protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DWS8, O15101, Q13719, Q15911, Q6ZP98
    2. XM_024450291.2XP_024306059.1  zinc finger homeobox protein 3 isoform X4

      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_017023251.3XP_016878740.1  zinc finger homeobox protein 3 isoform X3

    4. XM_047434167.1XP_047290123.1  zinc finger homeobox protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DWS8, O15101, Q13719, Q15911, Q6ZP98
    5. XM_047434165.1XP_047290121.1  zinc finger homeobox protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DWS8, O15101, Q13719, Q15911, Q6ZP98
    6. XM_047434168.1XP_047290124.1  zinc finger homeobox protein 3 isoform X2

    7. XM_047434169.1XP_047290125.1  zinc finger homeobox protein 3 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      78600697..79709756 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380395.1XP_054236370.1  zinc finger homeobox protein 3 isoform X1

    2. XM_054380399.1XP_054236374.1  zinc finger homeobox protein 3 isoform X4

    3. XM_054380398.1XP_054236373.1  zinc finger homeobox protein 3 isoform X3

    4. XM_054380396.1XP_054236371.1  zinc finger homeobox protein 3 isoform X1

    5. XM_054380394.1XP_054236369.1  zinc finger homeobox protein 3 isoform X1

    6. XM_054380397.1XP_054236372.1  zinc finger homeobox protein 3 isoform X2

    7. XM_054380393.1XP_054236368.1  zinc finger homeobox protein 3 isoform X1

    8. XM_054380400.1XP_054236375.1  zinc finger homeobox protein 3 isoform X5