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. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures. [provided by RefSeq, Aug 2008] See more...

Aliases for TBX6 Gene

Aliases for TBX6 Gene

  • T-Box Transcription Factor 6 2 3 5
  • T-Box Transcription Factor TBX6 3 4
  • T-Box Protein 6 3 4
  • T-Box 6 2 3
  • SCDO5 3
  • TBX6 5

External Ids for TBX6 Gene

Previous GeneCards Identifiers for TBX6 Gene

  • GC16P029057
  • GC16M030419
  • GC16M030095
  • GC16M030134
  • GC16M030004
  • GC16M030097
  • GC16M027758

Summaries for TBX6 Gene

Entrez Gene Summary for TBX6 Gene

  • 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. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures. [provided by RefSeq, Aug 2008]

GeneCards Summary for TBX6 Gene

TBX6 (T-Box Transcription Factor 6) is a Protein Coding gene. Diseases associated with TBX6 include Spondylocostal Dysostosis 5 and Scoliosis. Among its related pathways are Gene regulatory network modelling somitogenesis and Neural Crest Differentiation. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and RNA polymerase II activating transcription factor binding. An important paralog of this gene is TBX3.

UniProtKB/Swiss-Prot Summary for TBX6 Gene

  • T-box transcription factor that plays an essential role in the determination of the fate of axial stem cells: neural vs mesodermal. Acts in part by down-regulating, a specific enhancer (N1) of SOX2, to inhibit neural development. Seems to play also an essential role in left/right axis determination and acts through effects on Notch signaling around the node as well as through an effect on the morphology and motility of the nodal cilia (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TBX6 Gene

Genomics for TBX6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TBX6 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TBX6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TBX6

Top Transcription factor binding sites by QIAGEN in the TBX6 gene promoter:
  • Nkx2-5

Genomic Locations for TBX6 Gene

Genomic Locations for TBX6 Gene
chr16:30,085,793-30,091,927
(GRCh38/hg38)
Size:
6,135 bases
Orientation:
Minus strand
chr16:30,097,114-30,103,208
(GRCh37/hg19)
Size:
6,095 bases
Orientation:
Minus strand

Genomic View for TBX6 Gene

Genes around TBX6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBX6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBX6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBX6 Gene

Proteins for TBX6 Gene

  • Protein details for TBX6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95947-TBX6_HUMAN
    Recommended name:
    T-box transcription factor TBX6
    Protein Accession:
    O95947
    Secondary Accessions:
    • Q8TAS4
    • Q9HA44

    Protein attributes for TBX6 Gene

    Size:
    436 amino acids
    Molecular mass:
    47045 Da
    Quaternary structure:
    • Forms a dimeric complex with DNA (in vitro).

    Alternative splice isoforms for TBX6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBX6 Gene

Post-translational modifications for TBX6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for TBX6
  • Boster Bio Antibodies for TBX6
  • Santa Cruz Biotechnology (SCBT) Antibodies for TBX6

No data available for DME Specific Peptides for TBX6 Gene

Domains & Families for TBX6 Gene

Gene Families for TBX6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for TBX6 Gene

InterPro:
Blocks:
  • Transcription factor, T-box
  • Brachyury protein family signature
ProtoNet:

Suggested Antigen Peptide Sequences for TBX6 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ12268 fis, clone MAMMA1001627, highly similar to Homo sapiens transcription factor TBX6 (Q9HA44_HUMAN)
  • T-box transcription factor TBX6 (TBX6_HUMAN)
genes like me logo Genes that share domains with TBX6: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TBX6 Gene

Function for TBX6 Gene

Molecular function for TBX6 Gene

UniProtKB/Swiss-Prot Function:
T-box transcription factor that plays an essential role in the determination of the fate of axial stem cells: neural vs mesodermal. Acts in part by down-regulating, a specific enhancer (N1) of SOX2, to inhibit neural development. Seems to play also an essential role in left/right axis determination and acts through effects on Notch signaling around the node as well as through an effect on the morphology and motility of the nodal cilia (By similarity).
GENATLAS Biochemistry:
murine T-box gene Tbx6 (T,brachyury) homolog,expressed during gastrulation and in some adult tissues,including testis,involved in paraxial mesoderm formation and somitogenesis

Phenotypes From GWAS Catalog for TBX6 Gene

Gene Ontology (GO) - Molecular Function for TBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001085 RNA polymerase II transcription factor binding ISS --
GO:0001102 RNA polymerase II activating transcription factor binding IBA,ISS --
genes like me logo Genes that share ontologies with TBX6: view
genes like me logo Genes that share phenotypes with TBX6: view

Human Phenotype Ontology for TBX6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TBX6 Gene

MGI Knock Outs for TBX6:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBX6

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for TBX6 Gene

Localization for TBX6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBX6 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TBX6 gene
Compartment Confidence
nucleus 4
extracellular 2
cytoskeleton 2
cytosol 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IEA,IBA 21873635
genes like me logo Genes that share ontologies with TBX6: view

Pathways & Interactions for TBX6 Gene

genes like me logo Genes that share pathways with TBX6: view

Gene Ontology (GO) - Biological Process for TBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II ISS --
GO:0001570 vasculogenesis IBA --
GO:0001707 mesoderm formation IEA --
GO:0001708 cell fate specification IBA 21873635
GO:0001947 heart looping IBA 21873635
genes like me logo Genes that share ontologies with TBX6: view

No data available for SIGNOR curated interactions for TBX6 Gene

Drugs & Compounds for TBX6 Gene

No Compound Related Data Available

Transcripts for TBX6 Gene

mRNA/cDNA for TBX6 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBX6

Alternative Splicing Database (ASD) splice patterns (SP) for TBX6 Gene

No ASD Table

Relevant External Links for TBX6 Gene

GeneLoc Exon Structure for
TBX6

Expression for TBX6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TBX6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TBX6 Gene

This gene is overexpressed in Esophagus - Mucosa (x6.2).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TBX6

SOURCE GeneReport for Unigene cluster for TBX6 Gene:

Hs.198301

mRNA Expression by UniProt/SwissProt for TBX6 Gene:

O95947-TBX6_HUMAN
Tissue specificity: Expressed in fetal tail bud, posterior spinal tissue, intervertebral disk and testis. Also expressed in adult testis, kidney, lung, muscle and thymus.

Evidence on tissue expression from TISSUES for TBX6 Gene

  • Nervous system(4.4)
  • Blood(4.3)
  • Lymph node(4)
  • Spleen(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TBX6 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • eye
  • eyelid
  • face
  • head
  • neck
  • nose
  • skull
Thorax:
  • chest wall
  • lung
  • rib
  • rib cage
  • sternum
Pelvis:
  • pelvis
General:
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with TBX6: view

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for TBX6 Gene

Orthologs for TBX6 Gene

This gene was present in the common ancestor of animals.

Orthologs for TBX6 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TBX6 30 31
  • 99.46 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TBX6 30 31
  • 88.53 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TBX6 30 31
  • 87.31 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TBX6 31
  • 86 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Tbx6 30 17 31
  • 85.02 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tbx6 30
  • 84.79 (n)
Oppossum
(Monodelphis domestica)
Mammalia TBX6 31
  • 82 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TBX6 31
  • 33 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TBX6 31
  • 49 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii tbx6 31
  • 21 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Doc1 31 32
  • 33 (a)
ManyToMany
Doc3 31 32
  • 31 (a)
ManyToMany
Doc2 31 32
  • 28 (a)
ManyToMany
Species where no ortholog for TBX6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for TBX6 Gene

ENSEMBL:
Gene Tree for TBX6 (if available)
TreeFam:
Gene Tree for TBX6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TBX6: view image

Paralogs for TBX6 Gene

(15) SIMAP similar genes for TBX6 Gene using alignment to 2 proteins:

  • TBX6_HUMAN
  • Q9HA44_HUMAN
genes like me logo Genes that share paralogs with TBX6: view

Variants for TBX6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TBX6 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
694403 Pathogenic: Scoliosis 30,089,208(-) C/T MISSENSE_VARIANT
694404 Likely Pathogenic: Scoliosis 30,089,140(-) C/A MISSENSE_VARIANT
694405 Uncertain Significance: Scoliosis 30,089,124(-) T/A MISSENSE_VARIANT
694406 Pathogenic: Scoliosis 30,089,088(-) T/TCCC INFRAME_INSERTION
694407 Uncertain Significance: Scoliosis 30,089,065(-) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for TBX6 Gene

Structural Variations from Database of Genomic Variants (DGV) for TBX6 Gene

Variant ID Type Subtype PubMed ID
esv2758642 CNV gain 17122850
nsv1160384 CNV duplication 26073780
nsv833187 CNV loss 17160897

Variation tolerance for TBX6 Gene

Residual Variation Intolerance Score: 43.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.33; 41.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBX6 Gene

Human Gene Mutation Database (HGMD)
TBX6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBX6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBX6 Gene

Disorders for TBX6 Gene

MalaCards: The human disease database

(14) MalaCards diseases for TBX6 Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spondylocostal dysostosis 5
  • scdo5
scoliosis
dysostosis
  • dysostoses
spondylocostal dysostosis 3, autosomal recessive
  • spondylothoracic dysostosis
spondylocostal dysostosis, autosomal recessive
  • spondylocostal dysplasia
- elite association - COSMIC cancer census association via MalaCards
Search TBX6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TBX6_HUMAN
  • Spondylocostal dysostosis 5 (SCDO5) [MIM:122600]: A rare condition of variable severity characterized by vertebral and costal anomalies. The main feature include dwarfism, vertebral fusion, hemivertebrae, posterior rib fusion, reduced rib number, and other rib malformations. SCDO5 inheritance can be autosomal dominant or recessive. {ECO:0000269 PubMed:23335591, ECO:0000269 PubMed:25564734}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TBX6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with TBX6: view

No data available for Genatlas for TBX6 Gene

Publications for TBX6 Gene

  1. Identification, mapping, and phylogenomic analysis of four new human members of the T-box gene family: EOMES, TBX6, TBX18, and TBX19. (PMID: 9888994) Yi CH … Brook JD (Genomics 1999) 2 3 4
  2. The human TBX6 gene: cloning and assignment to chromosome 16p11.2. (PMID: 9933572) Papapetrou C … Edwards YH (Genomics 1999) 2 3 4
  3. Compound Heterozygosity for Null Mutations and a Common Hypomorphic Risk Haplotype in TBX6 Causes Congenital Scoliosis. (PMID: 28054739) Takeda K … Ikegawa S (Human mutation 2017) 3 4
  4. TBX6 null variants and a common hypomorphic allele in congenital scoliosis. (PMID: 25564734) Wu N … Zhang F (The New England journal of medicine 2015) 3 4
  5. Autosomal dominant spondylocostal dysostosis is caused by mutation in TBX6. (PMID: 23335591) Sparrow DB … Dunwoodie SL (Human molecular genetics 2013) 3 4

Products for TBX6 Gene

  • Signalway Proteins for TBX6

Sources for TBX6 Gene