GTF3A

general transcription factor IIIA, the group of General transcription factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 13:27424618-27435823

Links

ENSG00000122034 ∙ NCBI:2971 ∙ OMIM:600860 ∙ HGNC:4662 ∙ Uniprot:Q92664 ∙ 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 GTF3A gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF3A 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	11	0	0

Variants in GTF3A

This is a list of pathogenic ClinVar variants found in the GTF3A region.

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

Position	Type	Phenotype	Significance	ClinVar
13-27424753-G-A		not specified	Uncertain significance (Jan 20, 2023)
13-27424846-C-T		not specified	Uncertain significance (Jul 12, 2023)
13-27427116-G-A		not specified	Uncertain significance (Apr 07, 2023)
13-27429907-A-C		not specified	Uncertain significance (Dec 13, 2023)
13-27430555-A-C		not specified	Uncertain significance (Apr 27, 2022)
13-27432784-G-A		not specified	Uncertain significance (Jan 23, 2023)
13-27434819-G-A		not specified	Uncertain significance (Jan 18, 2022)
13-27434829-G-A		not specified	Likely benign (Sep 26, 2023)
13-27434837-T-C		not specified	Uncertain significance (Jul 05, 2023)
13-27434886-A-C		not specified	Uncertain significance (Sep 26, 2023)
13-27434900-C-T		not specified	Uncertain significance (Aug 17, 2022)
13-27435164-A-G		not specified	Uncertain significance (Jan 24, 2024)
13-27435165-T-A		not specified	Uncertain significance (Dec 03, 2021)
13-27435454-C-T		not specified	Uncertain significance (Mar 31, 2023)
13-27435459-T-A		not specified	Uncertain significance (Dec 12, 2023)
13-27435721-T-G		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF3A	protein_coding	protein_coding	ENST00000381140	9	11278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.78e-11	0.0324	124360	0	95	124455	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.135	195	190	1.03	0.00000978	2399
Missense in Polyphen		66	73.995	0.89196		932
Synonymous	0.541	62	67.7	0.916	0.00000344	642
Loss of Function	-0.218	16	15.1	1.06	7.30e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000270	0.000270
Ashkenazi Jewish	0.00359	0.00359
East Asian	0.000396	0.000389
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000287	0.000284
Middle Eastern	0.000396	0.000389
South Asian	0.000169	0.000163
Other	0.000674	0.000661

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in ribosomal large subunit biogenesis. Binds the approximately 50 base pairs internal control region (ICR) of 5S ribosomal RNA genes. It is required for their RNA polymerase III-dependent transcription and may also maintain the transcription of other genes (PubMed:24120868). Also binds the transcribed 5S RNA's (By similarity). {ECO:0000250|UniProtKB:P17842, ECO:0000269|PubMed:24120868}.
• Pathway: Adipogenesis;Gene expression (Transcription);the information processing pathway at the ifn beta enhancer;carm1 and regulation of the estrogen receptor;phosphoinositides and their downstream targets;chromatin remodeling by hswi/snf atp-dependent complexes;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 1 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription;IL4-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.0334
• ghis: 0.432

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf3a

Zebrafish Information Network

• Gene name: gtf3aa
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;transcription by RNA polymerase III;rRNA transcription;ribosomal large subunit biogenesis
• Cellular component: nucleus;nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;5S rRNA binding;metal ion binding