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Aliases for GTF2H2 Gene

Aliases for GTF2H2 Gene

  • General Transcription Factor IIH Subunit 2 2 3 5
  • General Transcription Factor IIH, Polypeptide 2, 44kDa 2 3
  • TFIIH Basal Transcription Factor Complex P44 Subunit 3 4
  • General Transcription Factor IIH Polypeptide 2 3 4
  • Basic Transcription Factor 2 44 KDa Subunit 3 4
  • BTF2 P44 3 4
  • BTF2P44 3 4
  • General Transcription Factor IIH, Polypeptide 2 (44kD Subunit) 2
  • General Transcription Factor IIH, Polypeptide 2, 44kD Subunit 3
  • T-BTF2P44 3
  • TFIIH 3
  • BTF2 3
  • P44 3

External Ids for GTF2H2 Gene

Previous GeneCards Identifiers for GTF2H2 Gene

  • GC05P069008
  • GC05P070422
  • GC05P068962
  • GC05M070366
  • GC05P065807
  • GC05M070330

Summaries for GTF2H2 Gene

Entrez Gene Summary for GTF2H2 Gene

  • This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. This gene is within the telomeric copy of the duplication. Deletion of this gene sometimes accompanies deletion of the neighboring SMN1 gene in spinal muscular atrophy (SMA) patients but it is unclear if deletion of this gene contributes to the SMA phenotype. This gene encodes the 44 kDa subunit of RNA polymerase II transcription initiation factor IIH which is involved in basal transcription and nucleotide excision repair. Transcript variants for this gene have been described, but their full length nature has not been determined. A second copy of this gene within the centromeric copy of the duplication has been described in the literature. It is reported to be different by either two or four base pairs; however, no sequence data is currently available for the centromeric copy of the gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for GTF2H2 Gene

GTF2H2 (General Transcription Factor IIH Subunit 2) is a Protein Coding gene. Diseases associated with GTF2H2 include Spinal Muscular Atrophy and Cockayne Syndrome. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and PEDF Induced Signaling. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and protein kinase activity. An important paralog of this gene is GTF2H2C.

UniProtKB/Swiss-Prot for GTF2H2 Gene

  • Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. The N-terminus interacts with and regulates XPD whereas an intact C-terminus is required for a successful escape of RNAP II form the promoter.

Gene Wiki entry for GTF2H2 Gene

Additional gene information for GTF2H2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GTF2H2 Gene

Genomics for GTF2H2 Gene

GeneHancer (GH) Regulatory Elements for GTF2H2 Gene

Promoters and enhancers for GTF2H2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I071066 Promoter 1 EPDnew Ensembl 550.8 +0.1 89 1.6 GTF2H2 NAIP
GH05I071063 Promoter 0.5 EPDnew 550.8 +4.6 4571 0.1 GTF2H2 NAIP
GH05I070952 Enhancer 0.2 Ensembl 5.9 +115.2 115188 0.6 GTF2H2 ENSG00000179978 SMN1 NAIP
GH05I071030 Enhancer 0.2 Ensembl 0.3 +36.2 36188 1.8 SERF1A NAIP GTF2H2
GH05I071025 Enhancer 0.2 Ensembl 0.3 +41.9 41889 0.4 NAIP GTF2H2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GTF2H2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GTF2H2 gene promoter:

Genomic Locations for GTF2H2 Gene

Genomic Locations for GTF2H2 Gene
35,020 bases
Minus strand

Genomic View for GTF2H2 Gene

Genes around GTF2H2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GTF2H2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GTF2H2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GTF2H2 Gene

Proteins for GTF2H2 Gene

  • Protein details for GTF2H2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    General transcription factor IIH subunit 2
    Protein Accession:
    Secondary Accessions:
    • Q15570
    • Q15571
    • Q9BS41

    Protein attributes for GTF2H2 Gene

    395 amino acids
    Molecular mass:
    44419 Da
    Quaternary structure:
    • Component of the TFIID-containing RNA polymerase II pre-initiation complex that is composed of TBP and at least GTF2A1, GTF2A2, GTF2E1, GTF2E2, GTF2F1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, GTF2B, TCEA1, ERCC2 and ERCC3 (PubMed:27193682). One of the 6 subunits forming the core-TFIIH basal transcription factor (PubMed:8194529, PubMed:11319235). The core-TFIIH basal transcription factor associates with the CAK complex composed of CDK7, CCNH/cyclin H and MNAT1 to form the TFIIH basal transcription factor (PubMed:9852112, PubMed:11319235). Interacts with XPB, XPD, GTF2H1 and GTF2H3 (PubMed:11319235). Interacts with varicella-zoster virus IE63 protein (PubMed:15843171).

    Three dimensional structures from OCA and Proteopedia for GTF2H2 Gene

    Alternative splice isoforms for GTF2H2 Gene


neXtProt entry for GTF2H2 Gene

Post-translational modifications for GTF2H2 Gene

No Post-translational modifications

No data available for DME Specific Peptides for GTF2H2 Gene

Domains & Families for GTF2H2 Gene

Gene Families for GTF2H2 Gene

Suggested Antigen Peptide Sequences for GTF2H2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the GTF2H2 family.
  • Belongs to the GTF2H2 family.
genes like me logo Genes that share domains with GTF2H2: view

Function for GTF2H2 Gene

Molecular function for GTF2H2 Gene

UniProtKB/Swiss-Prot Function:
Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. The N-terminus interacts with and regulates XPD whereas an intact C-terminus is required for a successful escape of RNAP II form the promoter.

Gene Ontology (GO) - Molecular Function for GTF2H2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding TAS 8194529
GO:0003700 DNA binding transcription factor activity NAS 8194529
GO:0004672 contributes_to protein kinase activity IDA 9852112
GO:0005515 protein binding IPI 7664335
GO:0008094 contributes_to DNA-dependent ATPase activity IDA 9852112
genes like me logo Genes that share ontologies with GTF2H2: view
genes like me logo Genes that share phenotypes with GTF2H2: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GTF2H2 Gene

Localization for GTF2H2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GTF2H2 Gene

Subcellular locations from

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 GTF2H2 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for GTF2H2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000438 core TFIIH complex portion of holo TFIIH complex IDA 27193682
GO:0000439 core TFIIH complex IEA --
GO:0005634 nucleus IEA,IDA 27193682
GO:0005654 nucleoplasm TAS --
GO:0005669 transcription factor TFIID complex IDA 27193682
genes like me logo Genes that share ontologies with GTF2H2: view

Pathways & Interactions for GTF2H2 Gene

SuperPathways for GTF2H2 Gene

SuperPathway Contained pathways
1 RNA Polymerase II Transcription Initiation And Promoter Clearance
2 Formation of HIV elongation complex in the absence of HIV Tat
3 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
4 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
5 HIV Life Cycle
genes like me logo Genes that share pathways with GTF2H2: view

Gene Ontology (GO) - Biological Process for GTF2H2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000717 nucleotide-excision repair, DNA duplex unwinding TAS --
GO:0002031 G-protein coupled receptor internalization IMP 15775968
GO:0006281 DNA repair IEA --
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
GO:0006289 nucleotide-excision repair IEA,IBA --
genes like me logo Genes that share ontologies with GTF2H2: view

No data available for SIGNOR curated interactions for GTF2H2 Gene

Drugs & Compounds for GTF2H2 Gene

(3) Drugs for GTF2H2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with GTF2H2: view

Transcripts for GTF2H2 Gene

mRNA/cDNA for GTF2H2 Gene

Unigene Clusters for GTF2H2 Gene

General transcription factor IIH, polypeptide 2, 44kDa:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GTF2H2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16
SP1: - -
SP2: -
SP3: -
SP5: - -
SP8: -

Relevant External Links for GTF2H2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for GTF2H2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GTF2H2 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GTF2H2 Gene

Protein tissue co-expression partners for GTF2H2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GTF2H2 Gene:


SOURCE GeneReport for Unigene cluster for GTF2H2 Gene:


mRNA Expression by UniProt/SwissProt for GTF2H2 Gene:

Tissue specificity: Widely expressed, with higher expression in skeletal muscle.

Evidence on tissue expression from TISSUES for GTF2H2 Gene

  • Nervous system(4.2)
  • Blood(4.1)
  • Skin(4.1)
genes like me logo Genes that share expression patterns with GTF2H2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for GTF2H2 Gene

Orthologs for GTF2H2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GTF2H2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia GTF2H2 33 34
  • 99.24 (n)
(Canis familiaris)
Mammalia -- 34
  • 97 (a)
GTF2H2 33
  • 91.98 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 94 (a)
-- 34
  • 88 (a)
(Bos Taurus)
Mammalia GTF2H2 34 33
  • 93 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 93 (a)
(Mus musculus)
Mammalia Gtf2h2 33 16 34
  • 90.72 (n)
(Rattus norvegicus)
Mammalia Gtf2h2 33
  • 88.1 (n)
(Gallus gallus)
Aves -- 34
  • 88 (a)
GTF2H2 33
  • 79.07 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia gtf2h2 33
  • 76.02 (n)
Str.6606 33
(Danio rerio)
Actinopterygii gtf2h2 33 34
  • 72.18 (n)
Dr.1630 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4755 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010559 33
  • 53.49 (n)
fruit fly
(Drosophila melanogaster)
Insecta Ssl1 35 33 34
  • 53.06 (n)
(Caenorhabditis elegans)
Secernentea CELE_T16H12.4 33
  • 52.47 (n)
T16H12.4 35 34
  • 42 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E09615g 33
  • 51.51 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SSL1 33 34 36
  • 49.18 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR338C 33
  • 46.36 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons GTF2H2 33
  • 49.29 (n)
(Oryza sativa)
Liliopsida Os04g0508900 33
  • 50.99 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ssl1 33
  • 49.58 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01831 33
  • 46.09 (n)
Species where no ortholog for GTF2H2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GTF2H2 Gene

Gene Tree for GTF2H2 (if available)
Gene Tree for GTF2H2 (if available)

Paralogs for GTF2H2 Gene

Paralogs for GTF2H2 Gene

(2) SIMAP similar genes for GTF2H2 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with GTF2H2: view

Variants for GTF2H2 Gene

Sequence variations from dbSNP and Humsavar for GTF2H2 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000023510 -- 71,106,604(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000052755 -- 71,106,000(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000330265 -- 71,063,919(-) A/C intron_variant
rs1000927154 -- 71,056,263(-) G/C intron_variant
rs1001024742 -- 71,099,122(-) A/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for GTF2H2 Gene

Variant ID Type Subtype PubMed ID
nsv950083 CNV deletion 24416366
nsv950086 CNV deletion 24416366
nsv980670 CNV duplication 23825009
nsv980677 CNV duplication 23825009
nsv433373 CNV gain 18776910
nsv433371 CNV gain 18776910
nsv428117 CNV gain+loss 18775914
nsv1122110 CNV deletion 24896259
nsv1074840 CNV deletion 25765185
nsv1074306 CNV deletion 25765185
nsv1073891 CNV deletion 25765185
nsv10707 CNV gain+loss 18304495
nsv1033366 CNV gain 25217958
esv999813 CNV gain 20482838
esv3894210 CNV loss 25118596
esv3890654 CNV loss 25118596
esv3890652 CNV loss 25118596
esv3890648 CNV loss 25118596
esv3890644 CNV gain+loss 25118596
esv3890643 CNV loss 25118596
esv3605385 CNV loss 21293372
esv3570183 CNV loss 25503493
esv32787 CNV gain+loss 17666407
esv2759348 CNV gain+loss 17122850
esv2673843 CNV deletion 23128226
esv22113 CNV gain+loss 19812545
esv1011240 CNV gain 20482838
dgv9872n54 CNV loss 21841781
dgv9870n54 CNV loss 21841781
dgv9868n54 CNV gain 21841781
dgv9867n54 CNV gain 21841781
dgv9866n54 CNV gain 21841781
dgv9864n54 CNV loss 21841781
dgv9863n54 CNV gain 21841781
dgv9862n54 CNV loss 21841781
dgv9861n54 CNV gain 21841781
dgv9860n54 CNV gain 21841781
dgv9859n54 CNV gain 21841781
dgv9857n54 CNV loss 21841781
dgv9854n54 CNV loss 21841781
dgv9845n54 CNV loss 21841781
dgv9844n54 CNV loss 21841781
dgv9838n54 CNV loss 21841781
dgv7e224 CNV loss 25118596
dgv5697n100 CNV gain+loss 25217958
dgv5696n100 CNV loss 25217958
dgv5695n100 CNV gain 25217958
dgv27n14 CNV loss 18776910
dgv134e203 CNV gain+loss 21179565
nsv830339 CNV gain 17160897
nsv821643 CNV loss 15273396
nsv7371 OTHER inversion 18451855
nsv598620 CNV loss 21841781
nsv598587 CNV gain+loss 21841781
nsv598561 CNV loss 21841781
nsv598539 CNV loss 21841781
nsv598538 CNV loss 21841781
nsv598537 CNV loss 21841781
nsv598536 CNV gain 21841781
nsv598535 CNV loss 21841781
nsv598534 CNV gain 21841781
nsv598533 CNV loss 21841781
nsv598523 CNV loss 21841781
nsv598462 CNV gain 21841781
nsv515025 CNV gain 21397061
nsv511290 CNV gain 21212237
nsv511107 OTHER complex 20534489
nsv511106 OTHER inversion 20534489
nsv508367 CNV deletion 20534489
nsv471489 CNV gain 19718026

Variation tolerance for GTF2H2 Gene

Gene Damage Index Score: 0.69; 14.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GTF2H2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GTF2H2 Gene

Disorders for GTF2H2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for GTF2H2 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
spinal muscular atrophy
  • sma
cockayne syndrome
  • cockayne's syndrome
muscular atrophy
  • amyotrophia
deafness, autosomal recessive 49
  • dfnb49
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for GTF2H2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GTF2H2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GTF2H2 Gene

Publications for GTF2H2 Gene

  1. p44 and p34 subunits of the BTF2/TFIIH transcription factor have homologies with SSL1, a yeast protein involved in DNA repair. (PMID: 8194529) Humbert S … Moncollin V (The EMBO journal 1994) 2 3 4 22 58
  2. A population-based study of genotypic and phenotypic variability in children with spinal muscular atrophy. (PMID: 19154529) Arkblad E … Darin N (Acta paediatrica (Oslo, Norway : 1992) 2009) 3 22 44 58
  3. A multicopy transcription-repair gene, BTF2p44, maps to the SMA region and demonstrates SMA associated deletions. (PMID: 9063743) Carter TA … Gilliam TC (Human molecular genetics 1997) 3 4 22 58
  4. Near-atomic resolution visualization of human transcription promoter opening. (PMID: 27193682) He Y … Nogales E (Nature 2016) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for GTF2H2 Gene

Sources for GTF2H2 Gene

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