GeneBe

GTF2F2

general transcription factor IIF subunit 2, the group of General transcription factor IIF complex subunits

Basic information

Region (hg38): 13:45120510-45284893

Links

ENSG00000188342 ∙ NCBI:2963 ∙ OMIM:189969 ∙ HGNC:4653 ∙ Uniprot:P13984 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GTF2F2 gene.

  • not_specified (45 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2F2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004128.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
23
clinvar
 23
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 23 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GTF2F2protein_codingprotein_codingENST00000340473 8163588
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.0002010.9791257250181257430.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.29821220.6720.000005791591
Missense in Polyphen1944.9920.4223605
Synonymous-0.5764843.21.110.00000197450
Loss of Function2.05918.50.4860.00000111211

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001200.000120
Ashkenazi Jewish0.000.00
East Asian0.0003940.000381
Finnish0.000.00
European (Non-Finnish)0.00004420.0000440
Middle Eastern0.0003940.000381
South Asian0.00006580.0000653
Other0.0001640.000163

dbNSFP

Source: dbNSFP

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. This subunit shows ATP-dependent DNA- helicase activity. {ECO:0000269|PubMed:2477704}.;
Pathway
Basal transcription factors - Homo sapiens (human);Eukaryotic Transcription Initiation;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;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;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
0.118

Intolerance Scores

loftool
0.343
rvis_EVS
-0.16
rvis_percentile_EVS
41.25

Haploinsufficiency Scores

pHI
0.160
hipred
Y
hipred_score
0.763
ghis
0.593

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.702

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Gtf2f2
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;RNA metabolic process;positive regulation of transcription elongation from RNA polymerase II promoter;snRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
Cellular component
nucleus;nucleoplasm;transcription factor TFIIF complex;microtubule cytoskeleton;transcriptional preinitiation complex
Molecular function
DNA binding;helicase activity;protein binding;ATP binding