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    TBX5 T-box transcription factor 5 [ Homo sapiens (human) ]

    Gene ID: 6910, updated on 17-Jun-2024

    Summary

    Official Symbol
    TBX5provided by HGNC
    Official Full Name
    T-box transcription factor 5provided by HGNC
    Primary source
    HGNC:HGNC:11604
    See related
    Ensembl:ENSG00000089225 MIM:601620; AllianceGenome:HGNC:11604
    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
    HOS
    Summary
    This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene is closely linked to related family member T-box 3 (ulnar mammary syndrome) on human chromosome 12. The encoded protein may play a role in heart development and specification of limb identity. Mutations in this gene have been associated with Holt-Oram syndrome, a developmental disorder affecting the heart and upper limbs. Several transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in heart (RPKM 12.5), placenta (RPKM 8.8) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TBX5 in Genome Data Viewer
    Location:
    12q24.21
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (114353911..114408442, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (114330644..114385180, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (114791716..114846247, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369995 Neighboring gene glutamate-ammonia ligase pseudogene 5 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24844 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24865 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:114601036-114602235 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:114676508-114676718 Neighboring gene Sharpr-MPRA regulatory region 11920 Neighboring gene long intergenic non-protein coding RNA 2459 Neighboring gene CRE9 enhancer downstream of TBX5 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:114723717-114724462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114739578-114740104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114740105-114740631 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:114773645-114774145 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:114843151-114843837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114843876-114844376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:114847097-114847637 Neighboring gene uncharacterized LOC105369998 Neighboring gene CRE16 enhancer upstream of TBX5 Neighboring gene TBX5 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114876822-114877445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114878069-114878691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114878692-114879313 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:114881262-114881765 Neighboring gene RN7SK pseudogene 216

    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
    Holt-Oram syndrome
    MedGen: C0265264 OMIM: 142900 GeneReviews: Holt-Oram Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-07-29)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-29)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
    EBI GWAS Catalog
    Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction.
    EBI GWAS Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
    EBI GWAS Catalog
    Genome-wide association studies of the PR interval in African Americans.
    EBI GWAS Catalog
    Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.
    EBI GWAS Catalog
    Genome-wide association study identifies three susceptibility loci for laryngeal squamous cell carcinoma in the Chinese population.
    EBI GWAS Catalog
    Genome-wide association study of blood pressure and hypertension.
    EBI GWAS Catalog
    Genome-wide association study of PR interval.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Identification of a novel percent mammographic density locus at 12q24.
    EBI GWAS Catalog
    Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Novel loci associated with PR interval in a genome-wide association study of 10 African American cohorts.
    EBI GWAS Catalog
    Several common variants modulate heart rate, PR interval and QRS duration.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in atrial septum morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in atrioventricular bundle cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in atrioventricular node cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in atrioventricular node cell fate commitment ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in atrioventricular valve morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_positive_effect bundle of His cell to Purkinje myocyte communication by electrical coupling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in bundle of His development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cardiac left ventricle formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cardiac left ventricle formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cardiac muscle cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell fate specification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell migration involved in coronary vasculogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cell-cell signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_positive_effect cell-cell signaling involved in cardiac conduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in embryonic forelimb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic limb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endocardial cushion development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within forelimb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in heart development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lung development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in morphogenesis of an epithelium IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cardiac muscle cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of epithelial to mesenchymal transition TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in pattern specification process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in pericardium development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of positive regulation of cardiac conduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cardiac muscle cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cardioblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of positive regulation of cell communication by electrical coupling involved in cardiac conduction TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of gap junction assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of secondary heart field cardioblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_positive_effect regulation of atrial cardiac muscle cell membrane depolarization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sinoatrial node development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ventricular septum development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    PubMed 
    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 
    part_of protein-DNA complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    T-box transcription factor TBX5
    Names
    T-box 5
    T-box protein 5

    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_007373.1 RefSeqGene

      Range
      5001..59513
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_670

    mRNA and Protein(s)

    1. NM_000192.3NP_000183.2  T-box transcription factor TBX5 isoform 1

      See identical proteins and their annotated locations for NP_000183.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 4 both encode the same isoform (1).
      Source sequence(s)
      AC009260, AF221714, BC027942, DA863182
      Consensus CDS
      CCDS9173.1
      UniProtKB/Swiss-Prot
      A6ND77, O15301, Q96TB0, Q99593, Q9Y4I2
      UniProtKB/TrEMBL
      A8K3J6
      Related
      ENSP00000309913.4, ENST00000310346.8
      Conserved Domains (1) summary
      cd20189
      Location:54238
      T-box_TBX4_5-like; DNA-binding domain of T-box transcription factor 4 and 5, and related T-box proteins
    2. NM_080717.4NP_542448.1  T-box transcription factor TBX5 isoform 3

      See identical proteins and their annotated locations for NP_542448.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks the exon containing the translation start site compared to transcript variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AB051068, AC009260, AF221714, BC027942
      Consensus CDS
      CCDS9174.1
      UniProtKB/TrEMBL
      A8K3J6
      Related
      ENSP00000337723.5, ENST00000349716.9
      Conserved Domains (1) summary
      cd20189
      Location:4188
      T-box_TBX4_5-like; DNA-binding domain of T-box transcription factor 4 and 5, and related T-box proteins
    3. NM_181486.4NP_852259.1  T-box transcription factor TBX5 isoform 1

      See identical proteins and their annotated locations for NP_852259.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1 and 4 both encode the same isoform (1).
      Source sequence(s)
      AC009260, BC027942, CB960757
      Consensus CDS
      CCDS9173.1
      UniProtKB/Swiss-Prot
      A6ND77, O15301, Q96TB0, Q99593, Q9Y4I2
      UniProtKB/TrEMBL
      A8K3J6
      Related
      ENSP00000384152.3, ENST00000405440.7
      Conserved Domains (1) summary
      cd20189
      Location:54238
      T-box_TBX4_5-like; DNA-binding domain of T-box transcription factor 4 and 5, and related T-box proteins

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      114353911..114408442 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017019912.2XP_016875401.1  T-box transcription factor TBX5 isoform X1

      UniProtKB/TrEMBL
      A8K3J6
      Conserved Domains (1) summary
      cd00182
      Location:69257
      TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      114330644..114385180 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_080718.1: Suppressed sequence

      Description
      NM_080718.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.