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

    Gene ID: 6911, updated on 14-Nov-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30085793..30091924, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30368436..30374583, complement)
    RS_2024_09 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 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. 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
    2. The association analysis of TBX6 polymorphism with susceptibility to congenital scoliosis in a Chinese Han population. Fei Q, et al. Spine (Phila Pa 1976), 2010 Apr 20. PMID 20228709
    3. Autosomal dominant spondylocostal dysostosis is caused by mutation in TBX6. Sparrow DB, et al. Hum Mol Genet, 2013 Apr 15. PMID 23335591
    4. TBX6 null variants and a common hypomorphic allele in congenital scoliosis. Wu N, et al. N Engl J Med, 2015 Jan 22. PMID 25564734, Free PMC Article
    5. Progress and perspective of TBX6 gene in congenital vertebral malformations. Chen W, et al. Oncotarget, 2016 Aug 30. PMID 27437870, Free PMC Article

    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
    		not available

    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)

    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 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
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in 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_2024_08

    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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