GTF2F1

protein-coding

general transcription factor IIF subunit 1, the group of General transcription factor IIF complex subunits|MicroRNA protein coding host genes

Gene summary

Enables several functions, including RNA polymerase II general transcription initiation factor activity; enzyme binding activity; and promoter-specific chromatin binding activity. Involved in positive regulation of transcription by RNA polymerase II; response to virus; and transcription by RNA polymerase II. Located in nucleoplasm. Part of transcription factor TFIID complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_002096.3

Inheritance

—

ClinVar variants

U:103B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr19:6,379,572-6,393,981

External References & Databases

Ensembl (ENSG00000125651)

Transcript & Mutation Effects

hg38 • Region Span ~14.4 kb

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GenCC 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 GTF2F1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 93

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002096.3. 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			4 clinvar	2 clinvar	1 clinvar	7
missense			95 clinvar	2 clinvar		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar	1 clinvar		5
Total	0	0	103	5	1	109

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002096.3	RefSeq	NP_002087.2	13	MANE Select
ENST00000394456.10	Ensembl	ENSP00000377969.3	13	MANE Select
ENST00000593678.5	Ensembl	ENSP00000469091.1	10	Standard
ENST00000595047.5	Ensembl	ENSP00000471403.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Basal transcription factors - Homo sapiens (human)
FGFR2 alternative splicing
Signaling by FGFR2
Disease
RNA Pol II CTD phosphorylation and interaction with CE during HIV infection

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
transcription coactivator activity
RNA binding
protein binding
transcription factor binding

Cellular Component

nucleus
nucleoplasm
transcription factor TFIID complex
transcription factor TFIIF complex
cell junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394456
Coding exons: 13
Length: 14413
Individuals with no LoFs: 125668
Homozygous LoFs: 0
Heterozygous LoFs: 80
Defined: 125748
p: 0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.415	321	343	0.937	0.0000241	3419
Missense (PolyPhen)		141	160.3	0.87959		1659
Synonymous	-0.864	160	147	1.09	0.0000118	925
Loss of Function	2.53	13	27.2	0.477	0.00000125	339

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00044	0.00043	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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. {ECO:0000269|PubMed:10428810}.;

Recessive Scores

pRec: 0.122

Intolerance Scores

LoFtool: 0.699
RVIS EVS: -1.2
RVIS percentile EVS: 5.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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