GTF2A2

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

Basic information

Region (hg38): 15:59638062-59657541

Links

ENSG00000140307 ∙ NCBI:2958 ∙ OMIM:600519 ∙ HGNC:4647 ∙ Uniprot:P52657 ∙ 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 GTF2A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2A2 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in GTF2A2

This is a list of pathogenic ClinVar variants found in the GTF2A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-59639139-G-A		not specified	Uncertain significance (Dec 05, 2024)
15-59639152-C-T		not specified	Uncertain significance (Oct 29, 2024)
15-59642213-A-G		not specified	Uncertain significance (Oct 12, 2024)
15-59642217-C-A		not specified	Uncertain significance (Mar 29, 2023)
15-59642235-C-T		not specified	Uncertain significance (Jul 14, 2024)
15-59650685-T-A		not specified	Uncertain significance (Jul 23, 2024)
15-59650764-T-C		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2A2	protein_coding	protein_coding	ENST00000396060	4	19480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0261	0.801	125723	0	6	125729	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.983	34	54.4	0.625	0.00000246	716
Missense in Polyphen		5	17.393	0.28746		234
Synonymous	0.0735	21	21.4	0.980	0.00000111	204
Loss of Function	1.02	3	5.62	0.534	2.38e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity. {ECO:0000269|PubMed:11030333}.
• Pathway: Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Eukaryotic Transcription Initiation;Disease;Signal Transduction;Gene expression (Transcription);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 Promoter Escape;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;ESR-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.603
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.325
• hipred: Y
• hipred_score: 0.800
• ghis: 0.660

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf2a2

Gene ontology

• Biological process: transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;viral process;snRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;positive regulation of DNA-binding transcription factor activity;RNA polymerase II preinitiation complex assembly
• Cellular component: nucleoplasm;transcription factor TFIID complex;transcription factor TFIIA complex;cell junction
• Molecular function: RNA polymerase II repressing transcription factor binding;transcription coactivator activity;protein binding;transcription factor binding;TBP-class protein binding;protein homodimerization activity;protein heterodimerization activity