GTF2F2

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

Basic information

Region (hg38): 13:45120509-45284893

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.

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.

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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10			10
Total	0	0	22	0	0

Variants in GTF2F2

This is a list of pathogenic ClinVar variants found in the GTF2F2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-45120684-C-T		not specified	Uncertain significance (Dec 20, 2022)
13-45120720-A-G		not specified	Uncertain significance (Aug 09, 2021)
13-45136733-G-A		not specified	Uncertain significance (Mar 15, 2024)
13-45136797-G-A		not specified	Uncertain significance (Mar 01, 2023)
13-45149781-G-A		not specified	Uncertain significance (Mar 29, 2023)
13-45151724-A-G		not specified	Uncertain significance (Oct 18, 2021)
13-45151730-T-C		not specified	Uncertain significance (Jul 12, 2023)
13-45151783-C-G		not specified	Uncertain significance (May 20, 2024)
13-45193822-A-G		not specified	Uncertain significance (Jan 24, 2023)
13-45193909-A-C		not specified	Uncertain significance (Jun 18, 2021)
13-45193990-A-G		not specified	Uncertain significance (Apr 13, 2022)
13-45194056-C-T		not specified	Uncertain significance (Sep 20, 2023)
13-45194057-G-A		not specified	Uncertain significance (Jan 22, 2024)
13-45194081-C-G		not specified	Uncertain significance (Aug 02, 2023)
13-45194119-T-A		not specified	Uncertain significance (Jan 04, 2022)
13-45194300-G-C		not specified	Uncertain significance (Jan 02, 2024)
13-45194359-G-A		not specified	Uncertain significance (Aug 26, 2022)
13-45194539-T-C		not specified	Uncertain significance (Jun 04, 2024)
13-45207438-G-A		not specified	Uncertain significance (Nov 02, 2023)
13-45207444-A-G		not specified	Uncertain significance (Apr 25, 2022)
13-45267276-G-T		not specified	Uncertain significance (May 24, 2023)
13-45267341-C-G		not specified	Uncertain significance (Mar 17, 2023)
13-45267357-A-T		not specified	Uncertain significance (Jul 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2F2	protein_coding	protein_coding	ENST00000340473	8	163588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000201	0.979	125725	0	18	125743	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	82	122	0.672	0.00000579	1591
Missense in Polyphen		19	44.992	0.4223		605
Synonymous	-0.576	48	43.2	1.11	0.00000197	450
Loss of Function	2.05	9	18.5	0.486	0.00000111	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000394	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.000394	0.000381
South Asian	0.0000658	0.0000653
Other	0.000164	0.000163

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gtf2f2

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