TCF20 transcription factor 20 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TCF20provided by HGNC
Official Full Name: transcription factor 20provided by HGNC
Primary source: HGNC:HGNC:11631
See related: Ensembl:ENSG00000100207 MIM:603107; AllianceGenome:HGNC:11631
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: AR1; SPBP; DDVIBA; TCF-20
Summary: 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]
Expression: Ubiquitous expression in testis (RPKM 9.0), thyroid (RPKM 8.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.2; 22q13.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (42160013..42343537, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (42639511..42824582, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (42556019..42679933, complement)

Chromosome 22 - NC_000022.11 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
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?

Diagnosis and clinical presentation of two individuals with a rare TCF20 pathogenic variant.
Title: Diagnosis and clinical presentation of two individuals with a rare TCF20 pathogenic variant.
Rare and de novo duplications containing TCF20 are associated with a neurodevelopmental disorder.
Title: Rare and de novo duplications containing TCF20 are associated with a neurodevelopmental disorder.
We provide valuable data regarding the prognosis and clinical manifestations of patients with variants in TCF20.
Title: Variants in TCF20 in neurodevelopmental disability: description of 27 new patients and review of literature.
TCF20 pathogenic variants are associated with a novel syndrome manifesting clinical characteristics similar to those observed in Smith-Magenis syndrome.
Title: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome.
Nonsense and one frameshift variant of TCF20 were identified the patients with intellectual disability and postnatal overgrowth. Such de novo variants of TCF20 may represent a novel differential diagnosis in the overgrowth syndrome spectrum.
Title: De novo nonsense and frameshift variants of TCF20 in individuals with intellectual disability and postnatal overgrowth.
mutations in TCF20 are associated with Autism spectrum disorders
Title: De novo and rare inherited mutations implicate the transcriptional coregulator TCF20/SPBP in autism spectrum disorder.
SPBP is a transcriptional coactivator of NRF2 regulating expression of the autophagy receptor p62.
Title: SPBP is a sulforaphane induced transcriptional coactivator of NRF2 regulating expression of the autophagy receptor p62/SQSTM1.
evolutionary conservation of chromatin binding of SPBP and RAI1
Title: A phylogenetic study of SPBP and RAI1: evolutionary conservation of chromatin binding modules.
Study has identified SPBP as a transcriptional coactivator of AR. We also show that Pax6 inhibits SPBP-mediated enhancement of AR activity on the AR target gene probasin promoter, a repression that was partly reversed by increased expression of SPBP.
Title: Pax6 represses androgen receptor-mediated transactivation by inhibiting recruitment of the coactivator SPBP.
Meta-analysis of gene-disease association. (HuGE Navigator)
Title: Prostate cancer risk-associated variants reported from genome-wide association studies: meta-analysis and their contribution to genetic Variation.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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
Developmental delay with variable intellectual impairment and behavioral abnormalities MedGen: C5193092 OMIM: 618430 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2019-06-26) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2019-06-26) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. 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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of transcription factor 20 (AR1) (PDCD2L) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-89209 (e-PCR)
- UniSTS:170518

SHGC-32817 (e-PCR)
- UniSTS:58452

RH47217 (e-PCR)
- UniSTS:18266

RH69793 (e-PCR)
- UniSTS:68998

Tcf20 (e-PCR), detects polymorphism
- UniSTS:496812

RH66208 (e-PCR)
- UniSTS:955

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in positive regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: transcription factor 20

Names: SPRE-binding protein; nuclear factor SPBP; stromelysin-1 PDGF-responsive element-binding protein; stromelysin-1 platelet-derived growth factor-responsive element binding protein

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_028982.3 RefSeqGene

Range

64690..188604

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1025

mRNA and Protein(s)

NM_001378418.1 → NP_001365347.1 transcription factor 20 isoform 1

Status: REVIEWED

Source sequence(s)

BX247885, Z83851

Consensus CDS

CCDS14033.1

UniProtKB/Swiss-Prot

A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0

UniProtKB/TrEMBL

W5ZR30

Related

ENSP00000503828.1, ENST00000677622.1

Conserved Domains (1) summary

cd15699
Location:1705 → 1932

ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
NM_005650.4 → NP_005641.1 transcription factor 20 isoform 1

See identical proteins and their annotated locations for NP_005641.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AB006630, BU732753, KF851355

Consensus CDS

CCDS14033.1

UniProtKB/Swiss-Prot

A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0

UniProtKB/TrEMBL

W5ZR30

Related

ENSP00000352463.3, ENST00000359486.8

Conserved Domains (1) summary

cd15699
Location:1705 → 1932

ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
NM_181492.3 → NP_852469.1 transcription factor 20 isoform 2

See identical proteins and their annotated locations for NP_852469.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the 3' coding region resulting in a frameshift, compared to variant 1. Isoform 2 has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

BX247885, Z83851

Consensus CDS

CCDS14032.1

UniProtKB/Swiss-Prot

Q9UGU0

Conserved Domains (1) summary

cd15699
Location:1705 → 1932

ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)