GTF2H2
general transcription factor IIH subunit 2, the group of General transcription factor IIH complex subunits|Nucleotide excision repair
Basic information
Region (hg38): 5:71035016-71067689
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2H2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 1 | 0 |
Variants in GTF2H2
This is a list of pathogenic ClinVar variants found in the GTF2H2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-71045459-G-A | not specified | Uncertain significance (Feb 10, 2023) | ||
| 5-71045465-G-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 5-71045469-C-A | not specified | Uncertain significance (Jan 16, 2024) | ||
| 5-71048057-C-G | not specified | Uncertain significance (May 27, 2022) | ||
| 5-71048078-T-G | not specified | Uncertain significance (Jun 28, 2022) | ||
| 5-71048109-C-T | Likely benign (Aug 25, 2017) | |||
| 5-71048794-C-T | not specified | Uncertain significance (Apr 15, 2024) | ||
| 5-71048822-A-T | not specified | Uncertain significance (May 14, 2024) | ||
| 5-71048839-G-A | not specified | Uncertain significance (May 18, 2023) | ||
| 5-71055382-T-G | not specified | Uncertain significance (Nov 08, 2022) | ||
| 5-71055389-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 5-71055407-A-T | not specified | Uncertain significance (Nov 11, 2024) | ||
| 5-71055419-C-T | not specified | Uncertain significance (Dec 08, 2023) | ||
| 5-71055436-G-T | not specified | Uncertain significance (May 13, 2024) | ||
| 5-71061304-A-G | not specified | Uncertain significance (Oct 20, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GTF2H2 | protein_coding | protein_coding | ENST00000330280 | 15 | 32733 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0155 | 0.711 | 122305 | 0 | 2 | 122307 | 0.00000818 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.641 | 28 | 39.3 | 0.712 | 0.00000199 | 2566 |
| Missense in Polyphen | 6 | 9.7723 | 0.61398 | 803 | ||
| Synonymous | 0.928 | 9 | 13.3 | 0.676 | 6.58e-7 | 722 |
| Loss of Function | 0.674 | 3 | 4.55 | 0.659 | 1.90e-7 | 334 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000666 | 0.0000666 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. In transcription, TFIIH has an essential role in transcription initiation. When the pre- initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module CAK controls the initiation of transcription. The N-terminus of GTF2H2 interacts with and regulates XPD whereas an intact C-terminus is required for a successful escape of RNAP II form the promoter. {ECO:0000269|PubMed:11319235, ECO:0000269|PubMed:27193682, ECO:0000269|PubMed:8194529, ECO:0000269|PubMed:9852112}.;
- Pathway
- Nucleotide excision repair - Homo sapiens (human);Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Eukaryotic Transcription Initiation;DNA Repair;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Formation of the HIV-1 Early Elongation Complex;Epigenetic regulation of gene expression;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;HIV Transcription Elongation;Formation of HIV elongation complex in the absence of HIV Tat;Generic Transcription Pathway;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II HIV Promoter Escape;RNA Polymerase II Pre-transcription Events;RNA Polymerase II Transcription Initiation;RNA Polymerase II Transcription Initiation And Promoter Clearance;RNA Pol II CTD phosphorylation and interaction with CE;Formation of RNA Pol II elongation complex ;RNA Polymerase I Promoter Clearance;HIV Transcription Initiation;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase II Transcription Elongation;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;RNA Polymerase II Promoter Escape;RNA Polymerase I Chain Elongation;AndrogenReceptor;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;mRNA Capping;Formation of the Early Elongation Complex;Formation of Incision Complex in GG-NER;Dual Incision in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Formation of TC-NER Pre-Incision Complex;Validated targets of C-MYC transcriptional repression;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.176
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.337
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gtf2h2
- Phenotype
Gene ontology
- Biological process
- G protein-coupled receptor internalization;transcription-coupled nucleotide-excision repair;nucleotide-excision repair;nucleotide-excision repair, preincision complex stabilization;nucleotide-excision repair, preincision complex assembly;nucleotide-excision repair, DNA incision, 5'-to lesion;regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;translation;protein phosphorylation;response to UV;nucleotide-excision repair, DNA incision;global genome nucleotide-excision repair;positive regulation of DNA helicase activity
- Cellular component
- core TFIIH complex portion of holo TFIIH complex;transcription factor TFIIH core complex;nucleus;nucleoplasm;transcription factor TFIID complex;transcription factor TFIIH holo complex;nuclear speck
- Molecular function
- nucleic acid binding;DNA-binding transcription factor activity;protein kinase activity;protein binding;DNA-dependent ATPase activity;translation factor activity, RNA binding;zinc ion binding;RNA polymerase II CTD heptapeptide repeat kinase activity;protein N-terminus binding