GTF2E1

general transcription factor IIE subunit 1, the group of General transcription factor IIE complex subunits

Basic information

Region (hg38): 3:120742636-120783069

Links

ENSG00000153767 ∙ NCBI:2960 ∙ OMIM:189962 ∙ HGNC:4650 ∙ Uniprot:P29083 ∙ 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 GTF2E1 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2E1 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					1	1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	1

Variants in GTF2E1

This is a list of pathogenic ClinVar variants found in the GTF2E1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-120750559-G-C		not specified	Uncertain significance (Nov 09, 2022)
3-120750719-G-A		not specified	Uncertain significance (Dec 11, 2023)
3-120750782-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-120750864-A-C		not specified	Uncertain significance (Apr 07, 2023)
3-120776532-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-120776598-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-120776634-G-C		not specified	Uncertain significance (Mar 01, 2024)
3-120776637-G-T		not specified	Uncertain significance (Nov 10, 2022)
3-120781065-T-G		not specified	Uncertain significance (Dec 11, 2023)
3-120781073-G-A		not specified	Uncertain significance (Apr 19, 2023)
3-120781090-G-A		not specified	Uncertain significance (Jan 04, 2024)
3-120781218-C-T			Benign (Aug 23, 2018)
3-120781352-G-A		not specified	Uncertain significance (Apr 25, 2022)
3-120781355-C-T		not specified	Uncertain significance (Jun 27, 2022)
3-120781366-A-G		not specified	Uncertain significance (Jan 24, 2023)
3-120781372-G-T		not specified	Uncertain significance (Mar 01, 2023)
3-120781397-C-A		not specified	Uncertain significance (Aug 23, 2021)
3-120781429-A-G		not specified	Uncertain significance (Jan 07, 2022)
3-120781432-G-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2E1	protein_coding	protein_coding	ENST00000283875	4	40433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.892	0.107	125739	0	5	125744	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	206	255	0.808	0.0000147	2901
Missense in Polyphen		54	81.955	0.6589		1018
Synonymous	-0.808	99	89.3	1.11	0.00000486	846
Loss of Function	3.25	2	16.0	0.125	0.00000100	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.
• Pathway: Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Eukaryotic Transcription Initiation;Disease;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;chromatin remodeling by hswi/snf atp-dependent complexes (Consensus)

Recessive Scores

• pRec: 0.184

Intolerance Scores

• loftool: 0.314
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94

Haploinsufficiency Scores

• pHI: 0.753
• hipred: Y
• hipred_score: 0.714
• ghis: 0.428

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf2e1

Gene ontology

• Biological process: transcriptional open complex formation at RNA polymerase II promoter;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;viral process;snRNA transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;transcription factor TFIID complex;transcription factor TFIIE complex;cytosol;transcriptional preinitiation complex
• Molecular function: RNA polymerase II complex binding;TFIIH-class transcription factor complex binding;protein binding;sequence-specific DNA binding;metal ion binding