GTF2B
general transcription factor IIB, the group of General transcription factors
Basic information
Region (hg38): 1:88852633-88891944
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 GTF2B 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in GTF2B
This is a list of pathogenic ClinVar variants found in the GTF2B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-88853241-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
| 1-88857476-C-T | not specified | Uncertain significance (Apr 12, 2022) | ||
| 1-88860252-T-C | not specified | Uncertain significance (Apr 26, 2023) | ||
| 1-88864019-G-A | not specified | Uncertain significance (Apr 17, 2024) | ||
| 1-88887291-T-C | not specified | Uncertain significance (Dec 11, 2023) | ||
| 1-88887297-C-T | not specified | Uncertain significance (Jul 28, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GTF2B | protein_coding | protein_coding | ENST00000370500 | 7 | 39013 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000115 | 0.956 | 125730 | 0 | 17 | 125747 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.53 | 84 | 179 | 0.468 | 0.00000929 | 2068 |
| Missense in Polyphen | 19 | 63.895 | 0.29736 | 721 | ||
| Synonymous | 0.0940 | 59 | 59.9 | 0.985 | 0.00000300 | 625 |
| Loss of Function | 1.82 | 9 | 17.1 | 0.526 | 0.00000117 | 171 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000181 | 0.000181 |
| Ashkenazi Jewish | 0.000101 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000882 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: General transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). Involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA (PubMed:1876184, PubMed:1946368, PubMed:1517211, PubMed:3818643, PubMed:3029109, PubMed:8413225, PubMed:8515820, PubMed:8516311, PubMed:8516312, PubMed:7601352, PubMed:9420329, PubMed:12931194, PubMed:27193682). Together with the TATA box-bound TBP forms the core initiation complex and provides a bridge between TBP and the Pol II-TFIIF complex (PubMed:8504927, PubMed:8413225, PubMed:8515820, PubMed:8516311, PubMed:8516312). Released from the PIC early following the onset of transcription during the initiation and elongation transition and reassociates with TBP during the next transcription cycle (PubMed:7601352). Associates with chromatin to core promoter- specific regions (PubMed:12931194, PubMed:24441171). Binds to two distinct DNA core promoter consensus sequence elements in a TBP- independent manner; these IIB-recognition elements (BREs) are localized immediately upstream (BREu), 5'-[GC][GC][GA]CGCC-3', and downstream (BREd), 5'-[GA]T[TGA][TG][GT][TG][TG]-3', of the TATA box element (PubMed:9420329, PubMed:16230532, PubMed:7675079, PubMed:10619841). Modulates transcription start site selection (PubMed:10318856). Exhibits also autoacetyltransferase activity that contributes to the activated transcription (PubMed:12931194). {ECO:0000269|PubMed:10318856, ECO:0000269|PubMed:10619841, ECO:0000269|PubMed:12931194, ECO:0000269|PubMed:1517211, ECO:0000269|PubMed:16230532, ECO:0000269|PubMed:1876184, ECO:0000269|PubMed:1946368, ECO:0000269|PubMed:24441171, ECO:0000269|PubMed:27193682, ECO:0000269|PubMed:3029109, ECO:0000269|PubMed:3818643, ECO:0000269|PubMed:7601352, ECO:0000269|PubMed:7675079, ECO:0000269|PubMed:8413225, ECO:0000269|PubMed:8504927, ECO:0000269|PubMed:8515820, ECO:0000269|PubMed:8516311, ECO:0000269|PubMed:8516312, ECO:0000269|PubMed:9420329}.;
- Pathway
- Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Eukaryotic Transcription Initiation;Disease;Gene expression (Transcription);the information processing pathway at the ifn beta enhancer;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;HIV Transcription Initiation;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;chromatin remodeling by hswi/snf atp-dependent complexes
(Consensus)
Recessive Scores
- pRec
- 0.350
Intolerance Scores
- loftool
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 61.28
Haploinsufficiency Scores
- pHI
- 0.927
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.556
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gtf2b
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- transcriptional start site selection at RNA polymerase II promoter;DNA-templated transcription, initiation;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;protein acetylation;viral process;histone acetylation;snRNA transcription by RNA polymerase II;positive regulation by host of viral transcription;positive regulation of viral transcription;RNA polymerase II preinitiation complex assembly;positive regulation of transcription initiation from RNA polymerase II promoter;positive regulation of core promoter binding;RNA polymerase II core complex assembly
- Cellular component
- nucleus;nucleoplasm;transcription factor TFIID complex;chromosome;nuclear body;protein-DNA complex;RNA polymerase II transcription factor complex;transcriptional preinitiation complex
- Molecular function
- RNA polymerase II core promoter sequence-specific DNA binding;RNA polymerase II complex binding;core promoter binding;RNA polymerase II complex recruiting activity;histone acetyltransferase activity;protein binding;transcription factor binding;zinc ion binding;acetyltransferase activity;TBP-class protein binding;thyroid hormone receptor binding;promoter-specific chromatin binding