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

Summary

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

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TBX6 as a cause of a combined skeletal-kidney dysplasia syndrome.
Title: TBX6 as a cause of a combined skeletal-kidney dysplasia syndrome.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2560 (e-PCR)
- UniSTS:37928

D15S1477 (e-PCR)
- UniSTS:474482

RH64991 (e-PCR)
- UniSTS:86456

TBX6_2324 (e-PCR)
- UniSTS:281046

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
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

NG_023283.1 RefSeqGene

Range

4961..11092

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

30085793..30091924 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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

XR_007064904.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

30368436..30374583 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

O95947, Q8TAS4, Q9HA44
XM_054313800.1 → XP_054169775.1 T-box transcription factor TBX6 isoform X1

UniProtKB/Swiss-Prot

O95947, Q8TAS4, Q9HA44
XM_054313799.1 → XP_054169774.1 T-box transcription factor TBX6 isoform X1

UniProtKB/Swiss-Prot

O95947, Q8TAS4, Q9HA44
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

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.