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

Gene ID: 6899, updated on 11-Sep-2019

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
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

Genomic context

See TBX1 in Genome Data Viewer
Location:
22q11.21
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (19756703..19783593)
105 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 uncharacterized LOC105372861 Neighboring gene glycoprotein Ib platelet subunit beta Neighboring gene VISTA enhancer hs515 Neighboring gene G protein subunit beta 1 like Neighboring gene ribosomal protein L7a pseudogene 70 Neighboring gene retrotransposon Gag like 10

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

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-03-22)

ClinGen Genome Curation Page
Haploinsufficency

Some evidence for dosage pathogenicity (Last evaluated (2012-03-22)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • FTO Obesity Variant Mechanism, organism-specific biosystem (from WikiPathways)
    FTO Obesity Variant Mechanism, organism-specific biosystemMechanism underlying the association of FTO locus variants and obesity. The wild type T allele at rs1421085 in the FTO locus comprises a protein-DNA binding motif for ARID5B that represses the transc...
  • Heart Development, organism-specific biosystem (from WikiPathways)
    Heart Development, organism-specific biosystemThis pathway has been largely adapted from an article by Deepak Srivastava, Cell. 2006 Sep 22;126(6):1037-48. In this pathway are known transcription factors, miRNAs and regulatory proteins that impa...
  • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
    Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
anterior/posterior pattern specification ISS
Inferred from Sequence or Structural Similarity
more info
 
aorta morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
artery morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
blood vessel development ISS
Inferred from Sequence or Structural Similarity
more info
 
blood vessel morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cell fate specification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell fate specification ISS
Inferred from Sequence or Structural Similarity
more info
 
cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to fibroblast growth factor stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to retinoic acid ISS
Inferred from Sequence or Structural Similarity
more info
 
cochlea morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
coronary artery morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
determination of left/right symmetry ISS
Inferred from Sequence or Structural Similarity
more info
 
ear morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic cranial skeleton morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic viscerocranium morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
enamel mineralization ISS
Inferred from Sequence or Structural Similarity
more info
 
epithelial cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
face morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
heart looping IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heart morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
lymph vessel development ISS
Inferred from Sequence or Structural Similarity
more info
 
mesenchymal cell apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
mesoderm development ISS
Inferred from Sequence or Structural Similarity
more info
 
middle ear morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
muscle cell fate commitment ISS
Inferred from Sequence or Structural Similarity
more info
 
muscle organ development ISS
Inferred from Sequence or Structural Similarity
more info
 
muscle organ morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
muscle tissue morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of mesenchymal cell apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neural crest cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
odontogenesis of dentin-containing tooth ISS
Inferred from Sequence or Structural Similarity
more info
 
outer ear morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
outflow tract morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
outflow tract septum morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
parathyroid gland development IMP
Inferred from Mutant Phenotype
more info
PubMed 
pattern specification process ISS
Inferred from Sequence or Structural Similarity
more info
 
pharyngeal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of MAPK cascade ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of epithelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of mesenchymal cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of tongue muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of animal organ morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
retinoic acid receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
semicircular canal morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
sensory perception of sound ISS
Inferred from Sequence or Structural Similarity
more info
 
social behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
soft palate development IMP
Inferred from Mutant Phenotype
more info
PubMed 
thymus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
thyroid gland development ISS
Inferred from Sequence or Structural Similarity
more info
 
tongue morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
vagus nerve morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

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)

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_005992.1NP_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/Swiss-Prot
    O43435
    UniProtKB/TrEMBL
    Q152R5
    Related
    ENSP00000352483.3, ENST00000359500.7
    Conserved Domains (1) summary
    pfam00907
    Location:112297
    T-box; T-box
  2. NM_080646.1NP_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
    O43435
    Related
    ENSP00000331176.7, ENST00000329705.11
    Conserved Domains (1) summary
    cd00182
    Location:109299
    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. NM_080647.1NP_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/Swiss-Prot
    O43435
    UniProtKB/TrEMBL
    D9ZGG0
    Related
    ENSP00000331791.4, ENST00000332710.8
    Conserved Domains (1) summary
    cd00182
    Location:109299
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_006724312.2XP_006724375.1  T-box transcription factor TBX1 isoform X2

    See identical proteins and their annotated locations for XP_006724375.1

    UniProtKB/Swiss-Prot
    O43435
    UniProtKB/TrEMBL
    D9ZGG0
    Conserved Domains (1) summary
    cd00182
    Location:109299
    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_017028926.1XP_016884415.1  T-box transcription factor TBX1 isoform X2

    UniProtKB/Swiss-Prot
    O43435
    UniProtKB/TrEMBL
    D9ZGG0
    Conserved Domains (1) summary
    cd00182
    Location:109299
    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_017028925.1XP_016884414.1  T-box transcription factor TBX1 isoform X1

    Related
    ENSP00000497003.1, ENST00000649276.1
  4. XM_017028928.1XP_016884417.1  T-box transcription factor TBX1 isoform X4

  5. XM_017028927.1XP_016884416.1  T-box transcription factor TBX1 isoform X3

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