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    TBX1 T-box transcription factor 1 [ Homo sapiens (human) ]

    Gene ID: 6899, updated on 27-Dec-2024

    Summary

    Official Symbol
    TBX1provided by HGNC
    Official Full Name
    T-box transcription factor 1provided by HGNC
    Primary source
    HGNC:HGNC:11592
    See related
    Ensembl:ENSG00000184058 MIM:602054; AllianceGenome:HGNC:11592
    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
    DGS; TGA; VCF; CAFS; CTHM; DGCR; DORV; VCFS; TBX1C; CATCH22
    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 product shares 98% amino acid sequence identity with the mouse ortholog. DiGeorge syndrome (DGS)/velocardiofacial syndrome (VCFS), a common congenital disorder characterized by neural-crest-related developmental defects, has been associated with deletions of chromosome 22q11.2, where this gene has been mapped. Studies using mouse models of DiGeorge syndrome suggest a major role for this gene in the molecular etiology of DGS/VCFS. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in testis (RPKM 1.4), prostate (RPKM 1.1) and 13 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See TBX1 in Genome Data Viewer
    Location:
    22q11.21
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19756703..19783593)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20133557..20160463)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19744226..19771116)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene SEPT5-GP1BB readthrough Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19710387-19711165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19711166-19711943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19713539-19714114 Neighboring gene uncharacterized LOC105372861 Neighboring gene Sharpr-MPRA regulatory region 13949 Neighboring gene glycoprotein Ib platelet subunit beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19730021-19730596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19730597-19731170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19734624-19735124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19744621-19745499 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19745779-19746288 Neighboring gene VISTA enhancer hs515 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19750215-19751157 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19758419-19758590 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19764062-19764563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19771036-19771536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19771537-19772037 Neighboring gene G protein subunit beta 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19784762-19785467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19786734-19787315 Neighboring gene ribosomal protein L7a pseudogene 70 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19794010-19794254 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19799088-19799263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19810945-19811459 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19831532-19832045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19832046-19832558 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19832559-19833071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19840887-19841505 Neighboring gene retrotransposon Gag like 10

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (23 hits/1298 screens)

    Associated conditions

    Description Tests
    Conotruncal heart malformations
    MedGen: C1857586 OMIM: 217095 GeneReviews: Not available
    Compare labs
    DiGeorge syndrome
    MedGen: C0012236 OMIM: 188400 GeneReviews: 22q11.2 Deletion Syndrome
    Compare labs
    Tetralogy of Fallot
    MedGen: C0039685 OMIM: 187500 GeneReviews: Not available
    Compare labs
    Velocardiofacial syndrome
    MedGen: C0220704 OMIM: 192430 GeneReviews: 22q11.2 Deletion Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2024-06-11)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2024-06-11)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.
    EBI GWAS Catalog
    GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by GOA

    Items 1 - 25 of 64
    Process Evidence Code Pubs
    involved_in angiogenesis  
    involved_in anterior/posterior pattern specification  
    involved_in aorta morphogenesis  
    involved_in artery morphogenesis  
    involved_in blood vessel development  
    involved_in blood vessel morphogenesis  
    involved_in cell fate specification  
    involved_in cell fate specification  
    involved_in cell population proliferation  
    involved_in cellular response to fibroblast growth factor stimulus  
    involved_in cellular response to retinoic acid  
    involved_in cochlea morphogenesis  
    involved_in coronary artery morphogenesis  
    involved_in determination of left/right symmetry  
    involved_in ear morphogenesis  
    involved_in embryonic cranial skeleton morphogenesis  
    involved_in embryonic viscerocranium morphogenesis PubMed 
    involved_in enamel mineralization  
    involved_in epithelial cell differentiation  
    involved_in face morphogenesis  
    involved_in heart development PubMed 
    involved_in heart morphogenesis  
    involved_in inner ear morphogenesis  
    involved_in lymph vessel development  
    involved_in mesenchymal cell apoptotic process  
    involved_in mesoderm development  
    involved_in middle ear morphogenesis  
    involved_in muscle cell fate commitment  
    involved_in muscle organ development  
    involved_in muscle organ morphogenesis  
    involved_in muscle tissue morphogenesis  
    involved_in negative regulation of cell differentiation  
    involved_in negative regulation of mesenchymal cell apoptotic process  
    involved_in neural crest cell migration  
    involved_in odontogenesis of dentin-containing tooth  
    involved_in outer ear morphogenesis  
    involved_in outflow tract morphogenesis  
    involved_in outflow tract septum morphogenesis  
    involved_in parathyroid gland development PubMed 
    involved_in pattern specification process  
    involved_in pharyngeal system development PubMed 
    involved_in positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of MAPK cascade  
    involved_in positive regulation of cell population proliferation  
    involved_in positive regulation of epithelial cell proliferation  
    involved_in positive regulation of mesenchymal cell proliferation  
    involved_in positive regulation of protein phosphorylation  
    involved_in positive regulation of tongue muscle cell differentiation  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in regulation of animal organ morphogenesis  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in regulation of transcription by RNA polymerase II PubMed 
    involved_in retinoic acid receptor signaling pathway  
    involved_in semicircular canal morphogenesis  
    involved_in sensory perception of sound  
    involved_in social behavior  
    involved_in soft palate development PubMed 
    involved_in somatic stem cell population maintenance  
    involved_in thymus development PubMed 
    involved_in thyroid gland development  
    involved_in tongue morphogenesis  
    involved_in vagus nerve morphogenesis  
    Items 1 - 25 of 64
    Component Evidence Code Pubs
    located_in chromatin  
    located_in chromatin  
    is_active_in nucleus  

    General protein information

    Preferred Names
    T-box transcription factor TBX1
    Names
    T-box 1 transcription factor C
    Testis-specific T-box protein
    brachyury

    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_009229.1 RefSeqGene

      Range
      5001..31891
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_226

    mRNA and Protein(s)

    1. NM_001379200.1 → NP_001366129.1  T-box transcription factor TBX1 isoform D

      Status: REVIEWED

      Source sequence(s)
      AC000091
      Consensus CDS
      CCDS93119.1
      UniProtKB/TrEMBL
      A0A3B3IS18
      Related
      ENSP00000497003.1, ENST00000649276.2
      Conserved Domains (1) summary
      cd20187
      Location:118 → 306
      T-box_TBX1_10-like; DNA-binding domain of T-box transcription factor 1 and 10, and related T-box proteifactors
    2. NM_005992.1 → NP_005983.1  T-box transcription factor TBX1 isoform B

      See identical proteins and their annotated locations for NP_005983.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (B) contains an alternate exon 9 and an additional exon 10 compared to variant C. It encodes an isoform (B) with the same N-terminal 336 aa, but an unique C-terminus with respect to isoforms A and C.
      Source sequence(s)
      AF012131
      Consensus CDS
      CCDS13765.1
      UniProtKB/TrEMBL
      Q152R5
      Related
      ENSP00000352483.3, ENST00000359500.7
      Conserved Domains (1) summary
      pfam00907
      Location:112 → 297
      T-box; T-box
    3. NM_080646.2 → NP_542377.1  T-box transcription factor TBX1 isoform A

      See identical proteins and their annotated locations for NP_542377.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (A) contains an alternate exon 9 compared to variant C, resulting in an isoform (A) with the same N-terminal 336 aa, but an unique C-terminus with respect to isoforms B and C.
      Source sequence(s)
      AF012130
      Consensus CDS
      CCDS13766.1
      UniProtKB/Swiss-Prot
      C6G493, C6G494, O43435, O43436, Q96RJ2
      Related
      ENSP00000331176.7, ENST00000329705.11
      Conserved Domains (1) summary
      cd20187
      Location:109 → 297
      T-box_TBX1_10-like; DNA-binding domain of T-box transcription factor 1 and 10, and related T-box proteifactors
    4. NM_080647.1 → NP_542378.1  T-box transcription factor TBX1 isoform C

      See identical proteins and their annotated locations for NP_542378.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (C) encodes the longest isoform (C) with the same N-terminal 336 aa, but an unique C-terminus with respect to isoforms A and B.
      Source sequence(s)
      AF373867
      Consensus CDS
      CCDS13767.1
      UniProtKB/TrEMBL
      D9ZGG0
      Related
      ENSP00000331791.4, ENST00000332710.8
      Conserved Domains (1) summary
      cd00182
      Location:109 → 299
      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 ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      19756703..19783593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006724312.3 → XP_006724375.1  T-box transcription factor TBX1 isoform X2

      See identical proteins and their annotated locations for XP_006724375.1

      UniProtKB/TrEMBL
      D9ZGG0
      Conserved Domains (1) summary
      cd00182
      Location:109 → 299
      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 ...
    2. XM_017028926.2 → XP_016884415.1  T-box transcription factor TBX1 isoform X2

      UniProtKB/TrEMBL
      D9ZGG0
      Conserved Domains (1) summary
      cd00182
      Location:109 → 299
      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 ...
    3. XM_017028927.2 → XP_016884416.2  T-box transcription factor TBX1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      20133557..20160463
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325879.1 → XP_054181854.1  T-box transcription factor TBX1 isoform X2

    2. XM_054325880.1 → XP_054181855.1  T-box transcription factor TBX1 isoform X2

    3. XM_054325878.1 → XP_054181853.1  T-box transcription factor TBX1 isoform X1

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