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TBX6 T-box transcription factor 6 [ Homo sapiens (human) ]

Gene ID: 6911, updated on 11-Apr-2024

Summary

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Official Symbol
TBX6provided by HGNC
Official Full Name
T-box transcription factor 6provided by HGNC
Primary source
HGNC:HGNC:11605
See related
Ensembl:ENSG00000149922 MIM:602427; AllianceGenome:HGNC:11605
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
SCDO5
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. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures. [provided by RefSeq, Aug 2008]
Expression
Ubiquitous expression in stomach (RPKM 1.7), urinary bladder (RPKM 1.0) and 23 other tissues See more
Orthologs
mouse all
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Genomic context

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See TBX6 in Genome Data Viewer
Location:
16p11.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30085793..30091924, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30368436..30374583, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30097114..30103245, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharaterized LOC112694756 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30076132-30076912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7350 Neighboring gene aldolase, fructose-bisphosphate A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10689 Neighboring gene protein phosphatase 4 catalytic subunit Neighboring gene ReSE screen-validated silencer GRCh37_chr16:30096821-30096985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30101709-30102582 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30107354-30107960 Neighboring gene yippee like 3 Neighboring gene YPEL3 divergent transcript Neighboring gene glycerophosphodiester phosphodiesterase domain containing 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. TBX6 as a cause of a combined skeletal-kidney dysplasia syndrome. Li G, et al. Am J Med Genet A, 2022 Dec. PMID 36161696, Free PMC Article
  2. Functional characteristics of a broad spectrum of TBX6 variants in Mayer-Rokitansky-Küster-Hauser syndrome. Ma C, et al. Genet Med, 2022 Nov. PMID 36112137
  3. An additional piece in the TBX6 gene dosage model: A novel nonsense variant in a fetus with severe spondylocostal dysostosis. Errichiello E, et al. Clin Genet, 2020 Dec. PMID 33058178
  4. TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease. Chen W, et al. Hum Mutat, 2020 Jan. PMID 31471994, Free PMC Article
  5. Bi-allelic loss of function variants of TBX6 causes a spectrum of malformation of spine and rib including congenital scoliosis and spondylocostal dysostosis. Otomo N, et al. J Med Genet, 2019 Sep. PMID 31015262

See all (39) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TBX6 as a cause of a combined skeletal-kidney dysplasia syndrome.
    Title: TBX6 as a cause of a combined skeletal-kidney dysplasia syndrome.
  2. Functional characteristics of a broad spectrum of TBX6 variants in Mayer-Rokitansky-Kuster-Hauser syndrome.
    Title: Functional characteristics of a broad spectrum of TBX6 variants in Mayer-Rokitansky-Küster-Hauser syndrome.
  3. Genetic variants of TBX6 and TBXT identified in patients with congenital scoliosis in Southern China.
    Title: Genetic variants of TBX6 and TBXT identified in patients with congenital scoliosis in Southern China.
  4. An additional piece in the TBX6 gene dosage model: A novel nonsense variant in a fetus with severe spondylocostal dysostosis.
    Title: An additional piece in the TBX6 gene dosage model: A novel nonsense variant in a fetus with severe spondylocostal dysostosis.
  5. Increased TBX6 gene dosages induce congenital cervical vertebral malformations in humans and mice.
    Title: Increased TBX6 gene dosages induce congenital cervical vertebral malformations in humans and mice.
  6. TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease.
    Title: TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease.
  7. Our study suggests that bi-allelic loss of function variants of TBX6 cause a spectrum of phenotypes including CS and SCD, depending on the severity of the loss of TBX6 function.
    Title: Bi-allelic loss of function variants of TBX6 causes a spectrum of malformation of spine and rib including congenital scoliosis and spondylocostal dysostosis.
  8. The type and distribution of vertebral column abnormalities in TBX6/Tbx6 compound inheritance implicate subtle perturbations in gene dosage as a cause of spine developmental birth defects responsible for about 10% of congenital scoliosis
    Title: TBX6-associated congenital scoliosis (TACS) as a clinically distinguishable subtype of congenital scoliosis: further evidence supporting the compound inheritance and TBX6 gene dosage model.
  9. association of variants in TBX6 with malformations of the mullerian ducts, is reported.
    Title: Sequence Variants in TBX6 Are Associated with Disorders of the Müllerian Ducts: An Update.
  10. our findings in the newly collected human Congenital vertebral malformations (CVMs) subjects and Tbx6 mouse models consistently support the contention that TBX6 compound inheritance causes CVMs, potentially via a gene dosage-dependent mechanism.
    Title: TBX6 compound inheritance leads to congenital vertebral malformations in humans and mice.
Submit: New GeneRIF Correction See all GeneRIFs (22)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Spondylocostal dysostosis 5
MedGen: C4083048 OMIM: 122600 GeneReviews: Spondylocostal Dysostosis, Autosomal Recessive
Compare labs

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
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 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-specific DNA-binding transcription factor binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in anatomical structure morphogenesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in cell fate specification IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heart looping IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mesoderm development TAS
Traceable Author Statement
more info
 PubMed 
involved_in mesodermal cell fate specification IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of neuron maturation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of neuron projection development IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in signal transduction involved in regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in somite rostral/caudal axis specification IEA
Inferred from Electronic Annotation
more info
  
involved_in vasculogenesis IBA
Inferred from Biological aspect of Ancestor
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
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
T-box transcription factor TBX6
Names
T-box 6
T-box protein 6

NCBI Reference Sequences (RefSeq)

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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_023283.1 RefSeqGene

    Range
    4961..11092
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004608.4 → NP_004599.2  T-box transcription factor TBX6

    See identical proteins and their annotated locations for NP_004599.2

    Status: REVIEWED

    Source sequence(s)
    AC012645, BC026031
    Consensus CDS
    CCDS10670.1
    UniProtKB/Swiss-Prot
    O95947, Q8TAS4, Q9HA44
    UniProtKB/TrEMBL
    X5DP27
    Related
    ENSP00000378650.2, ENST00000395224.7
    Conserved Domains (1) summary
    cd00182
    Location:90 → 277
    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_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
    30085793..30091924 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545926.4 → XP_011544228.1  T-box transcription factor TBX6 isoform X1

    See identical proteins and their annotated locations for XP_011544228.1

    UniProtKB/Swiss-Prot
    O95947, Q8TAS4, Q9HA44
    UniProtKB/TrEMBL
    X5DP27
    Conserved Domains (1) summary
    cd00182
    Location:90 → 277
    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_047434551.1 → XP_047290507.1  T-box transcription factor TBX6 isoform X1

    UniProtKB/Swiss-Prot
    O95947, Q8TAS4, Q9HA44
    Related
    ENSP00000279386.2, ENST00000279386.6

RNA

  1. XR_007064904.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    30368436..30374583 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054313801.1 → XP_054169776.1  T-box transcription factor TBX6 isoform X1

    UniProtKB/Swiss-Prot
    O95947, Q8TAS4, Q9HA44

  2. XM_054313800.1 → XP_054169775.1  T-box transcription factor TBX6 isoform X1

    UniProtKB/Swiss-Prot
    O95947, Q8TAS4, Q9HA44

  3. XM_054313799.1 → XP_054169774.1  T-box transcription factor TBX6 isoform X1

    UniProtKB/Swiss-Prot
    O95947, Q8TAS4, Q9HA44

  4. XM_054313802.1 → XP_054169777.1  T-box transcription factor TBX6 isoform X1

    UniProtKB/Swiss-Prot
    O95947, Q8TAS4, Q9HA44

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_080758.1: Suppressed sequence

    Description
    NM_080758.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95947.2 GenPept UniProtKB/Swiss-Prot:O95947

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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