GTF2H4 general transcription factor IIH subunit 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: GTF2H4provided by HGNC
Official Full Name: general transcription factor IIH subunit 4provided by HGNC
Primary source: HGNC:HGNC:4658
See related: Ensembl:ENSG00000213780 MIM:601760; AllianceGenome:HGNC:4658
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: P52; TFB2; TFIIH
Summary: Enables RNA polymerase II general transcription initiation factor activity. Involved in transcription by RNA polymerase II. Located in nuclear speck. Part of core TFIIH complex portion of holo TFIIH complex and transcription factor TFIID complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in appendix (RPKM 9.1), endometrium (RPKM 8.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (30908207..30914106)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (30772873..30778772)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (30875984..30881883)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Data demonstrates gene expression changes in differentially methylated GTF2H4 gene in patients with age-related macular degeneration.
Title: Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes.
functional genetic variants of GTF2H4 confer susceptibility to lung cancer.
Title: Genetic variant in DNA repair gene GTF2H4 is associated with lung cancer risk: a large-scale analysis of six published GWAS datasets in the TRICL consortium.
GTF2H4 variants may not be associated with susceptibility to aspirin-exacerbated respiratory disease and obstructive symptoms in asthmatics.
Title: Lack of association between GTF2H4 genetic variants and AERD development and FEV1 decline by aspirin provocation.
A single nucleotide polymorphism variant within the general transcription factor IIH, polypeptide 4 gene, GTF2H4, on chromosome 6p21.33 was significantly associated with MS
Title: Variation within DNA repair pathway genes and risk of multiple sclerosis.
Observational study of gene-disease association. (HuGE Navigator)
Title: Examination of genetic polymorphisms in newborns for signatures of sex-specific prenatal selection.
The frequency of congenital ichthyosis, collodion-baby type, was significantly higher in the TFIIH mutated group of trichothiodystrophy patients.
Title: New clinico-genetic classification of trichothiodystrophy.
Study demonstrates that an essential initiation factor, TFB2, forms a network of interactions with DNA near the transcription start site and facilitates promoter melting but may not be essential for promoter recognition.
Title: TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase.
For 6-4 photoproducts, we show that TFIIH complexes carrying an NH(2)-terminal XPD mutated protein are also deficient in recruitment of NER proteins downstream of TFIIH
Title: Defective transcription/repair factor IIH recruitment to specific UV lesions in trichothiodystrophy syndrome.
TFIIH changes subunit composition in response to DNA damage. The CAK is released from the core during nucleotide excision repair (NER).
Title: Nucleotide excision repair driven by the dissociation of CAK from TFIIH.
TAF7 interacts with the transcription factors, TFIIH and P-TEFb, resulting in the inhibition of their Pol II CTD kinase activities
Title: TFIID component TAF7 functionally interacts with both TFIIH and P-TEFb.

Submit: New GeneRIF Correction See all GeneRIFs (18)

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

EBI GWAS Catalog

Description
Genetic predictors of medically refractory ulcerative colitis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for serum complement C3 and C4 levels in healthy Chinese subjects. 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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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	TFIIH synergizes with HIV-1 Tat to induce transcription elongation from the HIV-1 LTR promoter	PubMed
	tat	TFIIH interacts with HIV-1 Tat as a component of the HIV-1 transcription preinitiation complex, but is released from the elongation complex which includes P-TEFb	PubMed
	tat	CAK/TFIIH is required for HIV-1 Tat-mediated transactivation of the HIV-1 LTR promoter	PubMed
	tat	Amino acids 1-48 of HIV-1 Tat, which includes the Tat activation domain, mediate the binding of Tat to CAK and the TFIIH complex through a direct interaction with CDK7 and possibly other TFIIH subunits, including p62 and ERCC3	PubMed
	tat	Interaction of HIV-1 Tat with TFIIH stimulates phosphorylation of Ser-5 of the RNA polymerase II C-terminal domain (CTD), which in turn also stimulates co-transcriptional capping of HIV-1 mRNA	PubMed
	tat	HIV-1 Tat interacts with the RNA polymerase II holoenzyme and transcription preinitiation complexes, which include TFIIH, during Tat-mediated transactivation of the HIV-1 LTR	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

MARC_23960-23961:1031924369:1 (e-PCR)
- UniSTS:268813

SHGC-85159 (e-PCR)
- UniSTS:104006

MARC_6551-6552:992007295:1 (e-PCR)
- UniSTS:231243

MARC_6551-6552:996689776:1 (e-PCR)
- UniSTS:231243

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATPase activator activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II general transcription initiation factor activity	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair	TAS Traceable Author Statement more info	PubMed
involved_in nucleotide-excision repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of core TFIIH complex portion of holo TFIIH complex	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of transcription factor TFIID complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription factor TFIIH core complex	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription factor TFIIH holo complex	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription factor TFIIH holo complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: general transcription factor IIH subunit 4

Names: BTF2 p52; TFIIH basal transcription factor complex p52 subunit; basic transcription factor 2 52 kDa subunit; general transcription factor IIH polypeptide 4; general transcription factor IIH, polypeptide 4, 52kDa

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.