GTF2F2
protein-codinggeneral transcription factor IIF subunit 2, the group of General transcription factor IIF complex subunits
Gene summary
Predicted to enable RNA polymerase II general transcription initiation factor activity. Involved in positive regulation of transcription by RNA polymerase II; transcription elongation by RNA polymerase II; and transcription initiation at RNA polymerase II promoter. Located in microtubule cytoskeleton and nucleoplasm. [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 ~164.4 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 GTF2F2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004128.3. 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 | 2 | 1 | 3 | |||
| missense | 26 | 26 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 32 | 1 | 0 | 33 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004119.1 | 8 | MANE Select | |
| Ensembl | ENSP00000340823.6 | 8 | MANE Select | |
| Ensembl | ENSP00000516507.1 | 3 | Standard | |
| Ensembl | ENSP00000553090.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Basal transcription factors - Homo sapiens (human)
- Eukaryotic Transcription Initiation
- FGFR2 alternative splicing
- Signaling by FGFR2
- Disease
Biological Process
- mRNA splicing, via spliceosome
- transcription by RNA polymerase II
- transcription initiation from RNA polymerase II promoter
- transcription elongation from RNA polymerase II promoter
- 7-methylguanosine mRNA capping
Molecular Function
- DNA binding
- helicase activity
- protein binding
- ATP binding
Cellular Component
- nucleus
- nucleoplasm
- transcription factor TFIIF complex
- microtubule cytoskeleton
- transcriptional preinitiation complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000340473
- Coding exons
- 8
- Length
- 163588
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125743
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.29 | 82 | 122 | 0.672 | 0.00000579 | 1591 |
| Missense (PolyPhen) | 19 | 44.992 | 0.4223 | 605 | ||
| Synonymous | -0.576 | 48 | 43.2 | 1.11 | 0.00000197 | 450 |
| Loss of Function | 2.05 | 9 | 18.5 | 0.486 | 0.00000111 | 211 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00039 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA- helicase activity. {ECO:0000269|PubMed:2477704}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- LoFtool
- 0.343
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.25
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.702
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |