GTF2F1
Basic information
Region (hg38): 19:6379571-6393981
Links
Phenotypes
GenCC
Source:
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 GTF2F1 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 | 2 | |||||
missense | 40 | 41 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 40 | 2 | 2 |
Variants in GTF2F1
This is a list of pathogenic ClinVar variants found in the GTF2F1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
19-6380286-C-T | not specified | Uncertain significance (Feb 06, 2024) | ||
19-6380324-C-T | not specified | Uncertain significance (Feb 14, 2023) | ||
19-6380339-C-T | not specified | Uncertain significance (Aug 22, 2023) | ||
19-6380376-C-T | not specified | Uncertain significance (Mar 11, 2024) | ||
19-6380456-C-T | not specified | Uncertain significance (Dec 17, 2023) | ||
19-6380457-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
19-6380574-C-T | not specified | Uncertain significance (Mar 20, 2024) | ||
19-6380609-G-T | not specified | Uncertain significance (Jan 04, 2024) | ||
19-6380615-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
19-6380642-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
19-6380657-C-T | not specified | Uncertain significance (Mar 29, 2022) | ||
19-6380931-G-A | not specified | Uncertain significance (Sep 07, 2022) | ||
19-6380961-C-T | not specified | Likely benign (Apr 06, 2024) | ||
19-6380969-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
19-6380978-C-G | not specified | Uncertain significance (Dec 11, 2023) | ||
19-6380979-G-A | not specified | Uncertain significance (Mar 16, 2022) | ||
19-6381023-T-C | not specified | Uncertain significance (Jan 08, 2024) | ||
19-6381164-C-G | not specified | Uncertain significance (Apr 13, 2022) | ||
19-6381187-C-T | not specified | Uncertain significance (Jun 30, 2022) | ||
19-6381368-G-A | not specified | Uncertain significance (Sep 07, 2022) | ||
19-6381371-T-G | not specified | Uncertain significance (Dec 16, 2023) | ||
19-6381382-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
19-6381383-G-A | not specified | Uncertain significance (Feb 14, 2024) | ||
19-6381401-C-T | not specified | Uncertain significance (Apr 06, 2023) | ||
19-6381430-G-A | not specified | Uncertain significance (Jun 12, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GTF2F1 | protein_coding | protein_coding | ENST00000394456 | 13 | 14413 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000726 | 0.996 | 125668 | 0 | 80 | 125748 | 0.000318 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.415 | 321 | 343 | 0.937 | 0.0000241 | 3419 |
Missense in Polyphen | 141 | 160.3 | 0.87959 | 1659 | ||
Synonymous | -0.864 | 160 | 147 | 1.09 | 0.0000118 | 925 |
Loss of Function | 2.53 | 13 | 27.2 | 0.477 | 0.00000125 | 339 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000605 | 0.000597 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.000142 | 0.000139 |
European (Non-Finnish) | 0.000442 | 0.000431 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000229 | 0.000229 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. {ECO:0000269|PubMed:10428810}.;
- Pathway
- Basal transcription factors - Homo sapiens (human);FGFR2 alternative splicing;Signaling by FGFR2;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;Signal Transduction;Formation of the HIV-1 Early Elongation Complex;Gene expression (Transcription);Signaling by FGFR;Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;Abortive elongation of HIV-1 transcript in the absence of Tat;HIV Transcription Elongation;HIV elongation arrest and recovery;the information processing pathway at the ifn beta enhancer;carm1 and regulation of the estrogen receptor;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;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;Viral Messenger RNA Synthesis;Influenza Viral RNA Transcription and Replication;Formation of RNA Pol II elongation complex ;Influenza Life Cycle;Influenza Infection;HIV Transcription Initiation;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;RNA Polymerase II Transcription Elongation;mRNA Splicing - Major Pathway;RNA Polymerase II Promoter Escape;AndrogenReceptor;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;TP53 Regulates Transcription of DNA Repair Genes;Signaling by Nuclear Receptors;Transcriptional Regulation by TP53;mRNA Capping;chromatin remodeling by hswi/snf atp-dependent complexes;Formation of the Early Elongation Complex;Estrogen-dependent gene expression;Signaling by Receptor Tyrosine Kinases;ESR-mediated signaling;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- loftool
- 0.699
- rvis_EVS
- -1.2
- rvis_percentile_EVS
- 5.83
Haploinsufficiency Scores
- pHI
- 0.314
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.642
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- 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
- Gtf2f1
- Phenotype
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;fibroblast growth factor receptor signaling pathway;response to virus;RNA metabolic process;negative regulation of protein binding;positive regulation of transcription elongation from RNA polymerase II promoter;snRNA transcription by RNA polymerase II;positive regulation of catalytic activity;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;transcription factor TFIID complex;transcription factor TFIIF complex;cell junction;protein-containing complex;intracellular membrane-bounded organelle
- Molecular function
- DNA binding;transcription coactivator activity;RNA binding;protein binding;transcription factor binding;phosphatase activator activity;protein phosphatase binding;protein domain specific binding;promoter-specific chromatin binding