This gene encodes a transcription factor that recognizes the platelet-derived growth factor-responsive element in the matrix metalloproteinase 3 promoter. The encoded protein is thought to be a transcriptional coactivator, enhancing the activity of transcription factors such as JUN and SP1. Mutations in this gene are associated with autism spectrum disorders. Alternative splici... See more...

Aliases for TCF20 Gene

Aliases for TCF20 Gene

  • Transcription Factor 20 2 3 4 5
  • SPBP 2 3 4
  • Stromelysin-1 Platelet-Derived Growth Factor-Responsive Element Binding Protein 2 3
  • Stromelysin-1 PDGF-Responsive Element-Binding Protein 3 4
  • SPRE-Binding Protein 3 4
  • Nuclear Factor SPBP 3 4
  • TCF-20 3 4
  • AR1 2 3
  • Transcription Factor 20 (AR1) 2
  • Protein AR1 4
  • KIAA0292 4
  • DDVIBA 3
  • TCF20 5

External Ids for TCF20 Gene

Previous GeneCards Identifiers for TCF20 Gene

  • GC22M039158
  • GC22M040786
  • GC22M040880
  • GC22M042556
  • GC22M025521

Summaries for TCF20 Gene

Entrez Gene Summary for TCF20 Gene

  • This gene encodes a transcription factor that recognizes the platelet-derived growth factor-responsive element in the matrix metalloproteinase 3 promoter. The encoded protein is thought to be a transcriptional coactivator, enhancing the activity of transcription factors such as JUN and SP1. Mutations in this gene are associated with autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

GeneCards Summary for TCF20 Gene

TCF20 (Transcription Factor 20) is a Protein Coding gene. Diseases associated with TCF20 include Developmental Delay With Variable Intellectual Impairment And Behavioral Abnormalities and Pectus Excavatum. Among its related pathways are TGF-Beta Pathway and WNT Signaling. Gene Ontology (GO) annotations related to this gene include transcription coactivator activity. An important paralog of this gene is RAI1.

UniProtKB/Swiss-Prot Summary for TCF20 Gene

  • Transcriptional activator that binds to the regulatory region of MMP3 and thereby controls stromelysin expression. It stimulates the activity of various transcriptional activators such as JUN, SP1, PAX6 and ETS1, suggesting a function as a coactivator.

Gene Wiki entry for TCF20 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TCF20 Gene

Genomics for TCF20 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TCF20 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J042343 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 -0.5 -488 2.2 EZH2 ZBTB10 FEZF1 BCL11B ZNF189 ZSCAN23 NRF1 ZBTB33 ZNF768 ZNF133 TCF20 NFAM1 LINC01315
GH22J042342 Promoter/Enhancer 0.7 Ensembl dbSUPER 250.7 +0.9 915 0.2 SP2 REST ZNF133 TCF20 LINC01315 HSALNG0135700-002 CYP2D7
GH22J041444 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 20.1 +897.2 897164 6.5 BCLAF1 SP1 ZNF207 MYC IKZF1 NCOR1 ZNF600 SIX5 SSRP1 JUND TOB2 ACO2 HSALNG0135639 LOC105373043 lnc-ACO2-1 EP300 L3MBTL2 PHF5A XRCC6 ZC3H7B
GH22J042612 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 21.8 -271.1 -271052 4.7 BCLAF1 SP1 ZNF207 ZNF654 MYC IKZF1 NCOR1 ZNF600 SIX5 SSRP1 POLDIP3 ENSG00000270022 RNU12 lnc-CYB5R3-1 RN7SKP80 RPL5P34 RRP7BP XRCC6 NAGA PHETA2
GH22J041831 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 19.5 +510.6 510557 4.5 BCLAF1 SP1 ZNF207 NCOR1 MYC IKZF1 ZNF600 JUND ZNF580 ZNF592 HSALNG0135666 SREBF2 SREBF2-AS1 piR-34985 piR-38684 piR-32612 piR-36461 piR-38064 piR-61267 POLDIP3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TCF20 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TCF20

Top Transcription factor binding sites by QIAGEN in the TCF20 gene promoter:
  • c-Ets-1
  • GATA-2
  • Nkx6-1
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2
  • STAT3
  • STAT4
  • STAT5A

Genomic Locations for TCF20 Gene

Latest Assembly
chr22:42,160,013-42,343,616
(GRCh38/hg38)
Size:
183,604 bases
Orientation:
Minus strand

Previous Assembly
chr22:42,556,019-42,679,933
(GRCh37/hg19 by Entrez Gene)
Size:
123,915 bases
Orientation:
Minus strand

chr22:42,556,019-42,739,622
(GRCh37/hg19 by Ensembl)
Size:
183,604 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr22(ALT_REF_LOCI_1):70,204-125,539 (-)
  • chr22(ALT_REF_LOCI_3):82,358-137,688 (-)
  • chr22(PATCHES):51,431-106,747 (-)

Genomic View for TCF20 Gene

Genes around TCF20 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TCF20 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TCF20 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TCF20 Gene

Proteins for TCF20 Gene

  • Protein details for TCF20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UGU0-TCF20_HUMAN
    Recommended name:
    Transcription factor 20
    Protein Accession:
    Q9UGU0
    Secondary Accessions:
    • A9JX12
    • O14528
    • Q13078
    • Q4V353
    • Q9H4M0

    Protein attributes for TCF20 Gene

    Size:
    1960 amino acids
    Molecular mass:
    211771 Da
    Quaternary structure:
    • Homodimer (Probable). Interacts with RNF4 and JUN (By similarity).
    SequenceCaution:
    • Sequence=AAC36392.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for TCF20 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TCF20 Gene

Post-translational modifications for TCF20 Gene

  • Ubiquitination at Lys844, Lys1086, and Lys1267
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TCF20 Gene

Domains & Families for TCF20 Gene

Gene Families for TCF20 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for TCF20 Gene

Suggested Antigen Peptide Sequences for TCF20 Gene

GenScript: Design optimal peptide antigens:
  • Stromelysin-1 PDGF-responsive element-binding protein (TCF20_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UGU0

UniProtKB/Swiss-Prot:

TCF20_HUMAN :
  • The atypical PHD domain functions as a negative modulator of cofactor binding.
Domain:
  • The atypical PHD domain functions as a negative modulator of cofactor binding.
genes like me logo Genes that share domains with TCF20: view

Function for TCF20 Gene

Molecular function for TCF20 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional activator that binds to the regulatory region of MMP3 and thereby controls stromelysin expression. It stimulates the activity of various transcriptional activators such as JUN, SP1, PAX6 and ETS1, suggesting a function as a coactivator.
GENATLAS Biochemistry:
transcription factor 20 (TCF20),highly homolog to Spbp,a murine activator of expression of stromelysin 1

Phenotypes From GWAS Catalog for TCF20 Gene

Gene Ontology (GO) - Molecular Function for TCF20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 17913746
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with TCF20: view
genes like me logo Genes that share phenotypes with TCF20: view

Human Phenotype Ontology for TCF20 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TCF20

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TCF20 Gene

Localization for TCF20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TCF20 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 TCF20 gene
Compartment Confidence
nucleus 5
mitochondrion 3
plasma membrane 2
extracellular 2
cytoskeleton 2
cytosol 2
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TCF20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 10995766
GO:0005654 nucleoplasm IDA --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with TCF20: view

Pathways & Interactions for TCF20 Gene

PathCards logo

SuperPathways for TCF20 Gene

SuperPathway Contained pathways
1 Human Embryonic Stem Cell Pluripotency
.50
.50
2 ERK Signaling
.58
.49
3 PAK Pathway
.36
4 TGF-Beta Pathway
.51
5 WNT Signaling
-
genes like me logo Genes that share pathways with TCF20: view

Pathways by source for TCF20 Gene

1 BioSystems pathway for TCF20 Gene
7 Qiagen pathways for TCF20 Gene
  • Epithelial Adherens Junctions
  • Factors Promoting Cardiogenesis in Vertebrates
  • Human Embryonic Stem Cell Pluripotency
  • ILK Signaling
  • JNK Pathway

Gene Ontology (GO) - Biological Process for TCF20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0045944 positive regulation of transcription by RNA polymerase II NAS 10995766
genes like me logo Genes that share ontologies with TCF20: view

No data available for SIGNOR curated interactions for TCF20 Gene

Drugs & Compounds for TCF20 Gene

No Compound Related Data Available

Transcripts for TCF20 Gene

mRNA/cDNA for TCF20 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TCF20

Alternative Splicing Database (ASD) splice patterns (SP) for TCF20 Gene

No ASD Table

Relevant External Links for TCF20 Gene

GeneLoc Exon Structure for
TCF20

Expression for TCF20 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TCF20 Gene

Protein differential expression in normal tissues from HIPED for TCF20 Gene

This gene is overexpressed in Heart (21.8), Peripheral blood mononuclear cells (17.7), CD8 Tcells (8.5), and Plasma (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TCF20 Gene



Protein tissue co-expression partners for TCF20 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TCF20

SOURCE GeneReport for Unigene cluster for TCF20 Gene:

Hs.475018

mRNA Expression by UniProt/SwissProt for TCF20 Gene:

Q9UGU0-TCF20_HUMAN
Tissue specificity: Expressed in most tissues, except in ovary and prostate. Isoform 1 is exclusively expressed in brain, heart and testis, and this form predominates in liver and kidney. Isoform 2 predominates in lung.

Evidence on tissue expression from TISSUES for TCF20 Gene

  • Nervous system(4.6)
  • Skin(2.7)
  • Kidney(2.4)
  • Intestine(2.2)
  • Heart(2.2)
  • Liver(2.2)
  • Blood(2.2)
  • Muscle(2.1)
  • Spleen(2)
genes like me logo Genes that share expression patterns with TCF20: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TCF20 Gene

Orthologs for TCF20 Gene

This gene was present in the common ancestor of animals.

Orthologs for TCF20 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TCF20 29 30
  • 99.37 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TCF20 29 30
  • 89.75 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Tcf20 29 16 30
  • 88.68 (n)
OneToMany
Zfp957 30
  • 54 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Tcf20 29
  • 88.6 (n)
Cow
(Bos Taurus)
Mammalia TCF20 29 30
  • 87.69 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TCF20 30
  • 87 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TCF20 30
  • 83 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TCF20 29 30
  • 75.79 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TCF20 30
  • 74 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tcf20 29
  • 60.91 (n)
Str.17635 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.16860 29
Zebrafish
(Danio rerio)
Actinopterygii tcf20 30
  • 22 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG5098 30
  • 16 (a)
OneToMany
Species where no ortholog for TCF20 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for TCF20 Gene

ENSEMBL:
Gene Tree for TCF20 (if available)
TreeFam:
Gene Tree for TCF20 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TCF20: view image
Alliance of Genome Resources:
Additional Orthologs for TCF20

Paralogs for TCF20 Gene

Paralogs for TCF20 Gene

genes like me logo Genes that share paralogs with TCF20: view

Variants for TCF20 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TCF20 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
1012705 Uncertain Significance: not provided 42,214,060(-) G/C
NM_001378418.1(TCF20):c.1246C>G (p.Pro416Ala)
MISSENSE
1030004 Uncertain Significance: Developmental delay with variable intellectual impairment and behavioral abnormalities 42,211,339(-) G/A
NM_001378418.1(TCF20):c.3967C>T (p.Pro1323Ser)
MISSENSE
1030005 Uncertain Significance: Developmental delay with variable intellectual impairment and behavioral abnormalities 42,211,290(-) G/A
NM_001378418.1(TCF20):c.4016C>T (p.Thr1339Ile)
MISSENSE
1030006 Uncertain Significance: Developmental delay with variable intellectual impairment and behavioral abnormalities 42,210,976(-) T/C
NM_001378418.1(TCF20):c.4330A>G (p.Lys1444Glu)
MISSENSE
915397 Uncertain Significance: Developmental delay with variable intellectual impairment and behavioral abnormalities 42,215,028(-) G/A
NM_001378418.1(TCF20):c.278C>T (p.Ala93Val)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TCF20 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TCF20 Gene

Variant ID Type Subtype PubMed ID
nsv3643 CNV insertion 18451855
nsv474702 CNV novel sequence insertion 20440878
nsv834210 CNV loss 17160897
nsv834211 CNV loss 17160897

Variation tolerance for TCF20 Gene

Residual Variation Intolerance Score: 0.349% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.94; 83.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TCF20 Gene

Human Gene Mutation Database (HGMD)
TCF20
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TCF20
Leiden Open Variation Database (LOVD)
TCF20

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TCF20 Gene

Disorders for TCF20 Gene

MalaCards: The human disease database

(23) MalaCards diseases for TCF20 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
developmental delay with variable intellectual impairment and behavioral abnormalities
  • ddviba
pectus excavatum
  • funnel chest
myoclonus
ptosis
  • blepharoptosis
autism
  • autistic disorder
- elite association - COSMIC cancer census association via MalaCards
Search TCF20 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TCF20_HUMAN
  • Developmental delay with variable intellectual impairment and behavioral abnormalities (DDVIBA) [MIM:618430]: An autosomal dominant disorder characterized by impaired intellectual development with speech difficulties, dysmorphic features, and behavioral abnormalities including autism spectrum disorder, attention deficit and hyperactivity. Additional variable features may include hypotonia, somatic overgrowth, macrocephaly, mild distal skeletal anomalies, sleep disturbances, movement disorders, and gastrointestinal issues, such as constipation. {ECO:0000269 PubMed:25228304, ECO:0000269 PubMed:27436265, ECO:0000269 PubMed:30739909, ECO:0000269 PubMed:30819258}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for TCF20

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TCF20: view

No data available for Genatlas for TCF20 Gene

Publications for TCF20 Gene

  1. The nuclear factor SPBP contains different functional domains and stimulates the activity of various transcriptional activators. (PMID: 10995766) Rekdal C … Johansen T (The Journal of biological chemistry 2000) 2 3 4 22
  2. Assignment of AR1, transcription factor 20 (TCF20), to human chromosome 22q13.3 with somatic cell hybrids and in situ hybridization. (PMID: 9730594) Rajadhyaksha A … Bina M (Cytogenetics and cell genetics 1998) 2 3 4 22
  3. De novo and rare inherited mutations implicate the transcriptional coregulator TCF20/SPBP in autism spectrum disorder. (PMID: 25228304) Babbs C … Wilkie AO (Journal of medical genetics 2014) 3 4 72
  4. Variants in TCF20 in neurodevelopmental disability: description of 27 new patients and review of literature. (PMID: 30739909) Torti E … Juusola J (Genetics in medicine : official journal of the American College of Medical Genetics 2019) 3 4
  5. De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. (PMID: 30819258) Vetrini F … Liu P (Genome medicine 2019) 3 4

Products for TCF20 Gene

Sources for TCF20 Gene