GTF2E1
protein-codinggeneral transcription factor IIE subunit 1, the group of General transcription factor IIE complex subunits
Gene summary
Enables RNA polymerase II general transcription initiation factor activity. Involved in RNA polymerase II preinitiation complex assembly. Located in nucleoplasm. Part of transcription factor TFIID complex. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~40.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GTF2E1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005513.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 52 | 1 | 53 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 1 | 1 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005504.2 | 4 | MANE Select | |
| Ensembl | ENSP00000283875.5 | 4 | MANE Select | |
| Ensembl | ENSP00000418808.1 | 2 | Standard | |
| Ensembl | ENSP00000417342.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Basal transcription factors - Homo sapiens (human)
- Viral carcinogenesis - Homo sapiens (human)
- Epstein-Barr virus infection - Homo sapiens (human)
- Eukaryotic Transcription Initiation
- Disease
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
Molecular Function
- RNA polymerase II complex binding
- TFIIH-class transcription factor complex binding
- protein binding
- sequence-specific DNA binding
- metal ion binding
Cellular Component
- nucleus
- nucleoplasm
- transcription factor TFIID complex
- transcription factor TFIIE complex
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000283875
- Coding exons
- 4
- Length
- 40433
- Individuals with no LoFs
- 125739
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125744
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.09 | 206 | 255 | 0.808 | 0.0000147 | 2901 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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.;
Recessive Scores
- pRec
- 0.184
Intolerance Scores
- LoFtool
- 0.314
- RVIS EVS
- 1.31
- RVIS percentile EVS
- 94
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |