GTF2F2

Summary

GTF2F2 (general transcription factor IIF subunit 2, HGNC:4653) is a protein-coding gene on chromosome 13q14.12-q14.13, encoding General transcription factor IIF subunit 2 (P13984). 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 is a selective cancer dependency (DepMap: 78.6% of cell lines).

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. Part of transcription factor TFIIF complex.

Source: NCBI Gene 2963 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 63 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• Cancer dependency (DepMap): dependent in 78.6% of screened cell lines
• MANE Select transcript: NM_004128

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4653
Approved symbol	GTF2F2
Name	general transcription factor IIF subunit 2
Location	13q14.12-q14.13
Locus type	gene with protein product
Status	Approved
Aliases	TFIIF, BTF4, RAP30
Ensembl gene	ENSG00000188342
Ensembl biotype	protein_coding
OMIM	189969
Entrez	2963

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 protein_coding, 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000340473, ENST00000461904, ENST00000494087, ENST00000706694, ENST00000706695, ENST00000706696, ENST00000706697, ENST00000883031, ENST00000883032, ENST00000912523, ENST00000912524

RefSeq mRNA: 1 — MANE Select: NM_004128 NM_004128

CCDS: CCDS9395

Canonical transcript exons

ENST00000340473 — 8 exons

Exon	Start	End
ENSE00001364027	45207424	45207505
ENSE00001370421	45151687	45151831
ENSE00001377067	45267233	45267376
ENSE00001389810	45136733	45136806
ENSE00001400657	45283442	45284893
ENSE00001479865	45120510	45120721
ENSE00001629288	45149770	45149788
ENSE00003470434	45252871	45252970

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 93.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.4298 / max 556.3045, expressed in 1820 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134952	38.9341	1820
134953	0.2003	112
134954	0.1965	85
134951	0.0989	23

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.54	gold quality
ventricular zone	UBERON:0003053	91.95	gold quality
ganglionic eminence	UBERON:0004023	91.33	gold quality
calcaneal tendon	UBERON:0003701	89.33	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.18	gold quality
skin of abdomen	UBERON:0001416	88.96	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.62	gold quality
skin of leg	UBERON:0001511	88.47	gold quality
adrenal tissue	UBERON:0018303	88.33	gold quality
cortical plate	UBERON:0005343	88.26	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	88.15	gold quality
muscle of leg	UBERON:0001383	88.04	gold quality
gastrocnemius	UBERON:0001388	87.81	gold quality
tibial nerve	UBERON:0001323	87.58	gold quality
muscle layer of sigmoid colon	UBERON:0035805	87.54	gold quality
heart left ventricle	UBERON:0002084	87.53	gold quality
monocyte	CL:0000576	87.27	gold quality
biceps brachii	UBERON:0001507	87.23	gold quality
zone of skin	UBERON:0000014	87.21	gold quality
cardiac ventricle	UBERON:0002082	87.10	gold quality
right adrenal gland cortex	UBERON:0035827	87.07	gold quality
right adrenal gland	UBERON:0001233	86.81	gold quality
left adrenal gland	UBERON:0001234	86.70	gold quality
mononuclear cell	CL:0000842	86.54	gold quality
left adrenal gland cortex	UBERON:0035825	86.51	gold quality
muscle organ	UBERON:0001630	86.45	gold quality
leukocyte	CL:0000738	86.25	gold quality
lower esophagus mucosa	UBERON:0035834	86.19	gold quality
embryo	UBERON:0000922	86.12	gold quality
mucosa of transverse colon	UBERON:0004991	86.09	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-10290	no	283.47
E-HCAD-5	no	2.14
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SMAD5, TBP

miRNA regulators (miRDB)

25 targeting GTF2F2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-6839-3P	99.39	68.86	1301
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-4796-5P	99.34	70.06	810
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-4777-3P	99.15	68.92	626
HSA-MIR-29B-1-5P	98.86	68.35	1364
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-26B-3P	98.71	67.49	1102
HSA-MIR-12120	98.05	68.44	1768
HSA-MIR-943	97.81	64.42	694
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-4703-3P	96.68	68.61	545
HSA-MIR-5195-5P	90.84	65.09	287
HSA-MIR-4523	85.64	61.16	64

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 78.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

• Results pinpoint critical residues for RNA polymerase II subunit 5 binding to RAP30 and/or to HBx, and identify these residues in both mammalian cells and in an in vitro binding assay. (PMID:16169872)
• NMR and thermodynamic studies further elucidate the complex molecular mechanism by which TFIIF and FCP1 cooperate for RNAPII recycling. (PMID:19215094)
• Data show that TFIIF has an important role in stabilizing TFIIB within the PIC and after transcription initiates. (PMID:21896726)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	gtf2f2b	ENSDARG00000006816
danio_rerio	gtf2f2a	ENSDARG00000069910
mus_musculus	Gtf2f2	ENSMUSG00000067995
rattus_norvegicus	Gtf2f2	ENSRNOG00000029316
drosophila_melanogaster	TfIIFbeta	FBGN0010421
caenorhabditis_elegans		WBGENE00012694

Protein

Protein identifiers

General transcription factor IIF subunit 2 — P13984 (reviewed: P13984)

Alternative names: General transcription factor IIF 30 kDa subunit, Transcription initiation factor IIF subunit beta, Transcription initiation factor RAP30

All UniProt accessions (2): P13984, A0A9L9PX76

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. Heterodimer of an alpha and a beta subunit. Interacts with HTATSF1 and GPBP1. Interacts with URI1. Interacts with GTF2B (via N-terminus); this interaction is inhibited in presence of GTF2F1. Part of TBP-based Pol II pre-initiation complex (PIC), in which Pol II core assembles with general transcription factors and other specific initiation factors including GTF2E1, GTF2E2, GTF2F1, GTF2F2, TCEA1, ERCC2, ERCC3, GTF2H2, GTF2H3, GTF2H4, GTF2H5, GTF2A1, GTF2A2, GTF2B and TBP; this large multi-subunit PIC complex mediates DNA unwinding and targets Pol II core to the transcription start site where the first phosphodiester bond forms.

Subcellular location. Nucleus.

Similarity. Belongs to the TFIIF beta subunit family.

RefSeq proteins (1): NP_004119* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003196	TFIIF_beta	Family
IPR011039	TFIIF_interaction	Homologous_superfamily
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily
IPR040450	TFIIF_beta_HTH	Domain
IPR040504	TFIIF_beta_N	Domain

Pfam: PF02270, PF17683

UniProt features (31 total): strand 13, helix 8, modified residue 6, binding site 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

58 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
1F3U	X-RAY DIFFRACTION	1.7
7NVU	ELECTRON MICROSCOPY	2.5
8WAV	ELECTRON MICROSCOPY	2.72
8WAX	ELECTRON MICROSCOPY	2.75
8WAZ	ELECTRON MICROSCOPY	2.76
8WAU	ELECTRON MICROSCOPY	2.78
7NVS	ELECTRON MICROSCOPY	2.8
8WAT	ELECTRON MICROSCOPY	2.82
8WAY	ELECTRON MICROSCOPY	2.85
7NVT	ELECTRON MICROSCOPY	2.9
8S52	ELECTRON MICROSCOPY	2.9
8WB0	ELECTRON MICROSCOPY	2.94
7ZWD	ELECTRON MICROSCOPY	3
7ZX8	ELECTRON MICROSCOPY	3
8WAW	ELECTRON MICROSCOPY	3.02
8S51	ELECTRON MICROSCOPY	3.1
7EGB	ELECTRON MICROSCOPY	3.3
7ZX7	ELECTRON MICROSCOPY	3.4
8S54	ELECTRON MICROSCOPY	3.4
8S55	ELECTRON MICROSCOPY	3.4
8S5N	ELECTRON MICROSCOPY	3.4
7EG9	ELECTRON MICROSCOPY	3.7
8BZ1	ELECTRON MICROSCOPY	3.8
5IYB	ELECTRON MICROSCOPY	3.9
5IYC	ELECTRON MICROSCOPY	3.9
5IYD	ELECTRON MICROSCOPY	3.9
7EGC	ELECTRON MICROSCOPY	3.9
8BVW	ELECTRON MICROSCOPY	4
7ENA	ELECTRON MICROSCOPY	4.07
7EGA	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P13984-F1	82.92	0.29

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (2): 227; 229

Post-translational modifications (6): 2, 22, 33, 137, 142, 248

Function

Pathways and Gene Ontology

Reactome pathways

59 pathways

ID	Pathway
R-HSA-112382	Formation of RNA Pol II elongation complex
R-HSA-113418	Formation of the Early Elongation Complex
R-HSA-167152	Formation of HIV elongation complex in the absence of HIV Tat
R-HSA-167158	Formation of the HIV-1 Early Elongation Complex
R-HSA-167160	RNA Pol II CTD phosphorylation and interaction with CE during HIV infection
R-HSA-167161	HIV Transcription Initiation
R-HSA-167162	RNA Polymerase II HIV Promoter Escape
R-HSA-167172	Transcription of the HIV genome
R-HSA-167200	Formation of HIV-1 elongation complex containing HIV-1 Tat
R-HSA-167238	Pausing and recovery of Tat-mediated HIV elongation
R-HSA-167242	Abortive elongation of HIV-1 transcript in the absence of Tat
R-HSA-167243	Tat-mediated HIV elongation arrest and recovery
R-HSA-167246	Tat-mediated elongation of the HIV-1 transcript
R-HSA-167287	HIV elongation arrest and recovery
R-HSA-167290	Pausing and recovery of HIV elongation
R-HSA-168325	Viral Messenger RNA Synthesis
R-HSA-674695	RNA Polymerase II Pre-transcription Events
R-HSA-6796648	TP53 Regulates Transcription of DNA Repair Genes
R-HSA-6803529	FGFR2 alternative splicing
R-HSA-6807505	RNA polymerase II transcribes snRNA genes
R-HSA-72086	mRNA Capping
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72165	mRNA Splicing - Minor Pathway
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73776	RNA Polymerase II Promoter Escape
R-HSA-73779	RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-HSA-75953	RNA Polymerase II Transcription Initiation
R-HSA-75955	RNA Polymerase II Transcription Elongation
R-HSA-76042	RNA Polymerase II Transcription Initiation And Promoter Clearance
R-HSA-77075	RNA Pol II CTD phosphorylation and interaction with CE

MSigDB gene sets: 176 (showing top): REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS, REACTOME_SIGNALING_BY_FGFR, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, MODULE_308, MODULE_229, REACTOME_HIV_INFECTION, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, TGIF_01, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, ZHAN_MULTIPLE_MYELOMA_HP_UP, MODULE_123, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, TGANTCA_AP1_C, GOBP_TRANSCRIPTION_INITIATION_AT_RNA_POLYMERASE_II_PROMOTER

GO Biological Process (4): transcription by RNA polymerase II (GO:0006366), transcription initiation at RNA polymerase II promoter (GO:0006367), transcription elongation by RNA polymerase II (GO:0006368), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (3): DNA binding (GO:0003677), RNA polymerase II general transcription initiation factor activity (GO:0016251), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription factor TFIIF complex (GO:0005674), microtubule cytoskeleton (GO:0015630), RNA polymerase II, holoenzyme (GO:0016591), RNA polymerase II transcription regulator complex (GO:0090575)

Reactome top-level categories

Rollup of top-9 pathways:

Category	Pathways
Transcription of the HIV genome	8
HIV Transcription Elongation	3
RNA Polymerase II Transcription Elongation	2
RNA Polymerase II Transcription	2
Late Phase of HIV Life Cycle	1
Tat-mediated elongation of the HIV-1 transcript	1
Influenza Viral RNA Transcription and Replication	1
Transcriptional Regulation by TP53	1
Signaling by FGFR2	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	4
DNA-templated transcription	1
DNA-templated transcription initiation	1
DNA-templated transcription elongation	1
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
nucleic acid binding	1
general transcription initiation factor activity	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
RNA polymerase II, holoenzyme	1
RNA polymerase II transcription regulator complex	1
cytoskeleton	1
nuclear DNA-directed RNA polymerase complex	1
transcription regulator complex	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

2192 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GTF2F2	GTF2F1	P35269	999
GTF2F2	GTF2B	Q00403	980
GTF2F2	TBP	P20226	962
GTF2F2	GTF2E2	P29084	951
GTF2F2	GTF2E1	P29083	905
GTF2F2	CTDP1	Q9Y5B0	883
GTF2F2	POLR2A	P24928	840
GTF2F2	TAF7	Q15545	817
GTF2F2	POLR2E	P19388	778
GTF2F2	TAF5	Q15542	735
GTF2F2	POLR2I	P36954	715
GTF2F2	TAF12	Q16514	713
GTF2F2	TAF6	P49848	706
GTF2F2	POLR2B	P30876	647
GTF2F2	ERCC3	P19447	606

IntAct

143 interactions, top by confidence:

A	B	Type	Score
GTF2F1	GTF2F2	psi-mi:“MI:0407”(direct interaction)	0.870
GTF2F1	GTF2F2	psi-mi:“MI:0915”(physical association)	0.870
GTF2F1	GTF2F2	psi-mi:“MI:0914”(association)	0.870
GTF2F1	GTF2F2	psi-mi:“MI:2364”(proximity)	0.870
GTF2F2	GTF2F1	psi-mi:“MI:2364”(proximity)	0.870
GTF2F2	GTF2F1	psi-mi:“MI:0915”(physical association)	0.870
POLR2E	POLR2D	psi-mi:“MI:0915”(physical association)	0.790

BioGRID (201): GTF2F2 (Affinity Capture-MS), GTF2F2 (Co-fractionation), GTF2F2 (Co-fractionation), GTF2F2 (Co-fractionation), GTF2F2 (Co-fractionation), GTF2F2 (Co-fractionation), GTF2F2 (Co-fractionation), SRRT (Co-fractionation), SUPT4H1 (Co-fractionation), SUPT5H (Co-fractionation), GTF2F2 (Affinity Capture-MS), KLF5 (Reconstituted Complex), GTF2F2 (Proximity Label-MS), GTF2F2 (Affinity Capture-MS), GTF2F2 (Affinity Capture-MS)

ESM2 similar proteins: A0JN61, A4QNE0, O35427, O60763, O60941, O70585, O75575, O88597, O95453, P11029, P11497, P13984, P41541, P41542, P69341, Q01750, Q05B58, Q0JNK5, Q13085, Q13901, Q14457, Q28559, Q2T9L9, Q32PE4, Q3ZBJ0, Q4A1L4, Q4A1L5, Q5R4J9, Q5R660, Q5R878, Q5RBU4, Q5SWU9, Q5ZHS3, Q5ZKS6, Q60482, Q6NRL4, Q80UM3, Q8BWQ6, Q8L5Y9, Q8NE86

Diamond homologs: P13984, P41896, P41900, Q01750, Q03123, Q2T9L9, Q8R0A0

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
GTF2F2	“up-regulates activity”	POLR2E	binding
GTF2F2	“up-regulates activity”	GTF2F1	binding
GTF2F2	“form complex”	TFIIF	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 129 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
FGFR2 mutant receptor activation	8	70.0×	2e-12
Signaling by FGFR2 IIIa TM	8	55.3×	2e-11
RNA Pol II CTD phosphorylation and interaction with CE during HIV infection	11	51.6×	2e-14
RNA Pol II CTD phosphorylation and interaction with CE	11	51.6×	2e-14
Abortive elongation of HIV-1 transcript in the absence of Tat	9	51.4×	2e-12
mRNA Capping	11	48.1×	3e-14
Formation of the Early Elongation Complex	11	42.5×	8e-14
Formation of the HIV-1 Early Elongation Complex	11	42.5×	8e-14

GO biological processes:

GO term	Partners	Fold	FDR
transcription initiation at RNA polymerase II promoter	6	20.2×	4e-04
transcription by RNA polymerase II	10	6.3×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

63 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2680 predictions. Top by Δscore:

Variant	Effect	Δscore
13:45120718:CAAGG:C	donor_loss	1.0000
13:45120719:AAGGT:A	donor_loss	1.0000
13:45120720:AGG:A	donor_loss	1.0000
13:45120722:G:C	donor_loss	1.0000
13:45136728:TTTA:T	acceptor_loss	1.0000
13:45136730:TAG:T	acceptor_loss	1.0000
13:45136731:A:AG	acceptor_gain	1.0000
13:45136731:A:T	acceptor_loss	1.0000
13:45136732:G:GA	acceptor_gain	1.0000
13:45136802:GCCAA:G	donor_gain	1.0000
13:45136803:CCAA:C	donor_gain	1.0000
13:45136804:CAA:C	donor_gain	1.0000
13:45136804:CAAG:C	donor_loss	1.0000
13:45136805:AA:A	donor_gain	1.0000
13:45136805:AAGT:A	donor_loss	1.0000
13:45136806:AGT:A	donor_loss	1.0000
13:45136807:G:GG	donor_gain	1.0000
13:45136808:TAAG:T	donor_loss	1.0000
13:45151681:TATTA:T	acceptor_loss	1.0000
13:45151683:TTA:T	acceptor_loss	1.0000
13:45151684:TAG:T	acceptor_loss	1.0000
13:45151685:A:AT	acceptor_loss	1.0000
13:45151829:CAGGT:C	donor_loss	1.0000
13:45151831:GGTA:G	donor_loss	1.0000
13:45151832:G:GC	donor_loss	1.0000
13:45151833:T:G	donor_loss	1.0000
13:45155247:GGGA:G	donor_gain	1.0000
13:45155248:G:GT	donor_gain	1.0000
13:45207417:A:AG	acceptor_gain	1.0000
13:45207421:A:AG	acceptor_gain	1.0000

AlphaMissense

1605 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:45120710:T:A	W19R	0.999
13:45120710:T:C	W19R	0.999
13:45120714:T:C	L20P	0.999
13:45136757:T:A	W31R	0.999
13:45136757:T:C	W31R	0.999
13:45136787:G:T	G41W	0.999
13:45136788:G:A	G41E	0.999
13:45207441:G:A	G108R	0.999
13:45207441:G:C	G108R	0.999
13:45207465:T:C	C116R	0.999
13:45267294:T:A	V183D	0.999
13:45267306:T:A	L187Q	0.999
13:45267306:T:C	L187P	0.999
13:45267317:T:C	F191L	0.999
13:45267318:T:C	F191S	0.999
13:45267319:T:A	F191L	0.999
13:45267319:T:G	F191L	0.999
13:45267335:T:G	Y197D	0.999
13:45267351:T:C	L202S	0.999
13:45283449:T:C	L213P	0.999
13:45283473:G:A	G221D	0.999
13:45283508:T:A	W233R	0.999
13:45283508:T:C	W233R	0.999
13:45136787:G:A	G41R	0.998
13:45136787:G:C	G41R	0.998
13:45151694:T:C	F56S	0.998
13:45207442:G:A	G108E	0.998
13:45207448:T:A	V110E	0.998
13:45207459:G:C	A114P	0.998
13:45207460:C:A	A114D	0.998

dbSNP variants (sampled 300 via entrez): RS1000031870 (13:45159858 A>G,T), RS1000033158 (13:45119827 T>C), RS1000034997 (13:45246887 A>T), RS1000046057 (13:45204565 C>T), RS1000117619 (13:45172624 G>A,C,T), RS1000167212 (13:45271852 C>T), RS1000169778 (13:45220252 A>G), RS1000200650 (13:45138316 C>T), RS1000207201 (13:45229749 T>G), RS1000215813 (13:45132574 G>A), RS1000226000 (13:45185978 G>T), RS1000240686 (13:45136127 C>G), RS1000247980 (13:45187770 G>GT), RS1000253147 (13:45125238 G>A), RS1000294718 (13:45135735 T>C)

Disease associations

OMIM: gene MIM:189969 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002806_10	Type 2 diabetes	1.000000e-06
GCST007448_21	Normal facial asymmetry (angle of surface orientation score)	3.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009751	facial asymmetry measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725079 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,538

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

3 potent at pChembl≥5 of 3 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.92	IC50	120	nM	MOLIBRESIB
5.14	Kd	7154	nM	CHEMBL3752910
5.11	ED50	7689	nM	CHEMBL3752910

PubChem BioAssay actives

2 with measured affinity, of 8 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2178520: Inhibition of GTF2F2 (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	ic50	0.1200	uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149865: Binding affinity to human GTF2F2 incubated for 45 mins by Kinobead based pull down assay	kd	7.1540	uM

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
Cyclosporine	increases expression, increases methylation	2
bisphenol F	affects cotreatment, increases methylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
nobiletin	decreases expression, decreases reaction	1
sodium arsenate	decreases expression, decreases reaction	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
abrine	increases expression	1
MT19c compound	increases expression	1
Temozolomide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Vorinostat	increases expression	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Caffeine	decreases phosphorylation	1
Diuron	decreases expression	1
Doxorubicin	affects expression	1
Ivermectin	decreases expression	1
Phenobarbital	affects expression	1
Phthalic Acids	decreases methylation	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Sodium Selenite	increases expression	1
Lactic Acid	decreases expression	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652907	Binding	Binding affinity to human GTF2F2 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.