GTF2F1

general transcription factor IIF subunit 1, the group of General transcription factor IIF complex subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:6379572-6393981

Links

ENSG00000125651

∙ NCBI:2962 ∙ OMIM:189968 ∙ HGNC:4652 ∙ Uniprot:P35269 ∙ 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 GTF2F1 gene.

not_specified (82 variants)
not_provided (4 variants)

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. These statistics are base on transcript: NM_000002096.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			79 clinvar	2 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)				1 clinvar		1
Total	0	0	79	5	1

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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. {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