GTF2H3
general transcription factor IIH subunit 3, the group of Nucleotide excision repair|General transcription factor IIH complex subunits
Basic information
Region (hg38): 12:123633739-123662604
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 GTF2H3 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 | 0 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 1 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 1 | 0 |
Variants in GTF2H3
This is a list of pathogenic ClinVar variants found in the GTF2H3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-123633740-G-C | Vanishing white matter disease | Uncertain significance (Jan 13, 2018) | ||
| 12-123633750-C-A | Vanishing white matter disease | Uncertain significance (Jan 13, 2018) | ||
| 12-123633765-C-T | Vanishing white matter disease | Uncertain significance (Jan 12, 2018) | ||
| 12-123633862-G-A | Likely benign (Dec 31, 2019) | |||
| 12-123639270-A-T | not specified | Uncertain significance (Dec 13, 2022) | ||
| 12-123639303-A-G | not specified | Uncertain significance (Feb 14, 2023) | ||
| 12-123648013-A-C | not specified | Uncertain significance (Dec 20, 2023) | ||
| 12-123651029-G-A | not specified | Uncertain significance (Jan 03, 2024) | ||
| 12-123652543-A-G | not specified | Uncertain significance (Nov 10, 2022) | ||
| 12-123654948-G-A | not specified | Uncertain significance (Oct 20, 2024) | ||
| 12-123654987-G-A | not specified | Uncertain significance (Aug 05, 2024) | ||
| 12-123655789-T-A | not specified | Uncertain significance (Dec 05, 2024) | ||
| 12-123655810-G-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 12-123659807-C-G | not specified | Uncertain significance (Jun 29, 2023) | ||
| 12-123659897-G-A | not specified | Uncertain significance (Nov 21, 2023) | ||
| 12-123659903-G-T | not specified | Uncertain significance (Aug 02, 2021) | ||
| 12-123659922-G-A | not specified | Uncertain significance (Dec 10, 2024) | ||
| 12-123660195-T-C | not specified | Uncertain significance (Nov 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GTF2H3 | protein_coding | protein_coding | ENST00000543341 | 13 | 28779 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.04e-8 | 0.762 | 125708 | 0 | 39 | 125747 | 0.000155 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.652 | 138 | 161 | 0.856 | 0.00000792 | 2024 |
| Missense in Polyphen | 42 | 49.675 | 0.8455 | 629 | ||
| Synonymous | -1.08 | 69 | 58.5 | 1.18 | 0.00000330 | 559 |
| Loss of Function | 1.41 | 15 | 22.1 | 0.678 | 0.00000108 | 268 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000890 | 0.000888 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000273 | 0.000272 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000969 | 0.0000967 |
| Middle Eastern | 0.000273 | 0.000272 |
| South Asian | 0.000204 | 0.000196 |
| Other | 0.000164 | 0.000163 |
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. {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;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)
Intolerance Scores
- loftool
- 0.431
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.58
Haploinsufficiency Scores
- pHI
- 0.297
- hipred
- Y
- hipred_score
- 0.617
- ghis
- 0.650
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.969
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gtf2h3
- Phenotype
Gene ontology
- Biological process
- DNA repair;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;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;nucleotide-excision repair, DNA incision;phosphorylation of RNA polymerase II C-terminal domain;global genome nucleotide-excision repair
- 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;transcriptional preinitiation complex
- Molecular function
- damaged DNA binding;DNA-binding transcription factor activity;protein kinase activity;protein binding;DNA-dependent ATPase activity;translation factor activity, RNA binding;RNA polymerase II CTD heptapeptide repeat kinase activity;metal ion binding;protein N-terminus binding