GTF2A1

general transcription factor IIA subunit 1, the group of Small nucleolar RNA protein coding host genes|General transcription factor IIA complex subunits

Basic information

Region (hg38): 14:81175452-81221377

Links

ENSG00000165417

∙ NCBI:2957 ∙ OMIM:600520 ∙ HGNC:4646 ∙ Uniprot:P52655 ∙ 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 GTF2A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2A1 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 clinvar			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 GTF2A1

This is a list of pathogenic ClinVar variants found in the GTF2A1 region.

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

Position	Phenotype	Significance	ClinVar
14-81180262-A-C	not specified	Uncertain significance (Jun 10, 2024)	3283041
14-81192559-T-A	not specified	Uncertain significance (Dec 09, 2023)	3103019
14-81192567-C-A	not specified	Uncertain significance (Jun 17, 2024)	2352301
14-81192585-T-G	not specified	Uncertain significance (Dec 19, 2022)	2407405
14-81192705-C-G	not specified	Uncertain significance (Oct 03, 2022)	2221400
14-81192745-A-G	not specified	Uncertain significance (Dec 27, 2023)	3103018
14-81192830-G-A	not specified	Uncertain significance (Jul 09, 2021)	2235537
14-81196211-T-C	not specified	Uncertain significance (Mar 02, 2023)	2455863

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2A1	protein_coding	protein_coding	ENST00000553612	9	45926

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00962	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	106	188	0.563	0.00000827	2474
Missense in Polyphen		45	90.325	0.4982		1202
Synonymous	0.933	57	66.7	0.855	0.00000312	691
Loss of Function	4.03	2	22.8	0.0879	9.75e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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, ECO:0000269|PubMed:16537915}.;
Pathway: Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Disease;Signal Transduction;Gene expression (Transcription);the information processing pathway at the ifn beta enhancer;carm1 and regulation of the estrogen receptor;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;chromatin remodeling by hswi/snf atp-dependent complexes;Estrogen-dependent gene expression;ESR-mediated signaling (Consensus)

Recessive Scores

pRec: 0.178

Intolerance Scores

loftool: 0.147
rvis_EVS: -0.19
rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

pHI: 0.816
hipred: Y
hipred_score: 0.682
ghis: 0.697

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gtf2a1
Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; skeleton phenotype; immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;snRNA transcription by RNA polymerase II;positive regulation of nucleic acid-templated transcription
Cellular component: nucleoplasm;transcription factor TFIID complex;transcription factor TFIIA complex;cytosol
Molecular function: RNA polymerase II repressing transcription factor binding;DNA binding;transcription coactivator activity;protein binding;transcription factor binding;TBP-class protein binding;protein heterodimerization activity