FUBP3

Summary

FUBP3 (far upstream element binding protein 3, HGNC:4005) is a protein-coding gene on chromosome 9q34.11-q34.12, encoding Far upstream element-binding protein 3 (Q96I24). May interact with single-stranded DNA from the far-upstream element (FUSE).

Enables single-stranded DNA binding activity. Involved in DNA-templated transcription; positive regulation of DNA-templated transcription; and positive regulation of gene expression. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus.

Source: NCBI Gene 8939 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 87 total
• Druggable target: yes
• MANE Select transcript: NM_003934

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4005
Approved symbol	FUBP3
Name	far upstream element binding protein 3
Location	9q34.11-q34.12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000107164
Ensembl biotype	protein_coding
OMIM	603536
Entrez	8939

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 16 protein_coding, 5 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000319725, ENST00000465949, ENST00000467100, ENST00000472006, ENST00000487406, ENST00000492199, ENST00000650723, ENST00000699747, ENST00000863494, ENST00000863495, ENST00000863496, ENST00000863497, ENST00000863498, ENST00000863499, ENST00000936134, ENST00000936135, ENST00000936136, ENST00000936137, ENST00000964142, ENST00000964143, ENST00000964144, ENST00000964145, ENST00000964146

RefSeq mRNA: 1 — MANE Select: NM_003934 NM_003934

CCDS: CCDS43893

Canonical transcript exons

ENST00000319725 — 19 exons

Exon	Start	End
ENSE00000868110	130617797	130617895
ENSE00000868111	130620354	130620458
ENSE00000984581	130634667	130634738
ENSE00001142533	130616355	130616517
ENSE00001142545	130612956	130613027
ENSE00001142682	130637014	130638352
ENSE00001325924	130614288	130614345
ENSE00001809698	130579577	130579764
ENSE00003277251	130632202	130632278
ENSE00003474044	130635999	130636126
ENSE00003510910	130623611	130623711
ENSE00003524972	130612456	130612505
ENSE00003543965	130631557	130631630
ENSE00003589683	130631942	130632022
ENSE00003599527	130622708	130622810
ENSE00003653985	130609954	130609987
ENSE00003656711	130626364	130626505
ENSE00003664435	130630628	130630788
ENSE00003666938	130595483	130595588

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 95.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.3119 / max 177.2784, expressed in 1822 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99024	32.3119	1822

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of uterus	UBERON:0009853	95.83	gold quality
right lobe of thyroid gland	UBERON:0001119	95.81	gold quality
left lobe of thyroid gland	UBERON:0001120	95.67	gold quality
thyroid gland	UBERON:0002046	95.22	gold quality
left ovary	UBERON:0002119	94.77	gold quality
germinal epithelium of ovary	UBERON:0001304	94.72	gold quality
right ovary	UBERON:0002118	94.71	gold quality
endocervix	UBERON:0000458	94.56	gold quality
left uterine tube	UBERON:0001303	94.29	gold quality
ventricular zone	UBERON:0003053	94.24	gold quality
ectocervix	UBERON:0012249	94.18	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.15	gold quality
popliteal artery	UBERON:0002250	94.12	gold quality
tibial artery	UBERON:0007610	94.12	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.12	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.06	gold quality
lower esophagus	UBERON:0013473	94.05	gold quality
penis	UBERON:0000989	94.02	gold quality
aorta	UBERON:0000947	93.95	gold quality
mucosa of stomach	UBERON:0001199	93.95	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.94	gold quality
right uterine tube	UBERON:0001302	93.91	gold quality
tibial nerve	UBERON:0001323	93.77	gold quality
thoracic aorta	UBERON:0001515	93.76	gold quality
descending thoracic aorta	UBERON:0002345	93.74	gold quality
ovary	UBERON:0000992	93.69	gold quality
ascending aorta	UBERON:0001496	93.69	gold quality
vagina	UBERON:0000996	93.68	gold quality
right lobe of liver	UBERON:0001114	93.53	gold quality
right coronary artery	UBERON:0001625	93.50	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.75
E-MTAB-10290	no	70.60
E-HCAD-5	no	2.24

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

Target	Regulation
FGF9	Unknown
MYC	Activation

miRNA regulators (miRDB)

113 targeting FUBP3, 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-6867-5P	100.00	82.21	3464
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505

Literature-anchored findings (GeneRIF, showing 4)

• study found that FBP1 as well as FBP3 are more frequently expressed in prostate and bladder cancer than in renal cancer; in addition, a positive correlation between levels of FBP1, FBP3 and c-Myc was exclusively detectable in renal cell carcinomas (PMID:19087307)
• The redistribution of FBP3 in subcellular compartments was observed after Enterovirus 71 (EV71) infection, and the decreased expression of FBP3 in host neuronal cells markedly inhibited viral replication. The results reveal various host proteins that potentially interact with the EV71 5’UTR in neuronal cells, and study found that FBP3 could serve as a positive regulator in host cells. (PMID:27291656)
• Long noncoding RNA CMPK2 promotes colorectal cancer progression by activating the FUBP3-c-Myc axis. (PMID:32203166)
• FUBP3 regulates chronic myeloid leukaemia progression through PRC2 complex regulated PAK1-ERK signalling. (PMID:36478132)

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
danio_rerio	fubp3	ENSDARG00000086896
mus_musculus	Fubp3	ENSMUSG00000026843
rattus_norvegicus	Fubp3	ENSRNOG00000009139
drosophila_melanogaster	ps	FBGN0261552
drosophila_melanogaster	mub	FBGN0262737
drosophila_melanogaster	Imp	FBGN0285926
caenorhabditis_elegans		WBGENE00003978
caenorhabditis_elegans		WBGENE00010908
caenorhabditis_elegans		WBGENE00013347
caenorhabditis_elegans		WBGENE00016489
caenorhabditis_elegans	fubl-4	WBGENE00019692

Paralogs (12): IGF2BP2 (ENSG00000073792), KHSRP (ENSG00000088247), PCBP4 (ENSG00000090097), NOVA2 (ENSG00000104967), IGF2BP3 (ENSG00000136231), NOVA1 (ENSG00000139910), IGF2BP1 (ENSG00000159217), FUBP1 (ENSG00000162613), HNRNPK (ENSG00000165119), PCBP1 (ENSG00000169564), PCBP3 (ENSG00000183570), PCBP2 (ENSG00000197111)

Protein

Protein identifiers

Far upstream element-binding protein 3 — Q96I24 (reviewed: Q96I24)

All UniProt accessions (3): Q96I24, A0A494C1K6, A0A8V8TNQ2

UniProt curated annotations — full annotation on UniProt →

Function. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression.

Subcellular location. Nucleus.

Tissue specificity. Detected in a number of cell lines.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96I24-1	1	yes
Q96I24-2	2

RefSeq proteins (1): NP_003925* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004087	KH_dom	Domain
IPR004088	KH_dom_type_1	Domain
IPR036612	KH_dom_type_1_sf	Homologous_superfamily

Pfam: PF00013

UniProt features (18 total): modified residue 5, domain 4, cross-link 2, splice variant 2, initiator methionine 1, chain 1, sequence conflict 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96I24-F1	66.40	0.23

Functional residue map

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

Post-translational modifications (7): 296, 539, 569, 15, 57, 2, 76

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 116 (showing top): LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, XU_RESPONSE_TO_TRETINOIN_DN, MORF_PPP6C, GARY_CD5_TARGETS_DN, SCHLOSSER_SERUM_RESPONSE_DN, GOCC_NEURON_PROJECTION, DORN_ADENOVIRUS_INFECTION_32HR_DN, MODULE_277, GOBP_RNA_LOCALIZATION, GOMF_SINGLE_STRANDED_DNA_BINDING, GOCC_RIBOSOME, NUYTTEN_EZH2_TARGETS_DN, GOCC_DENDRITIC_SHAFT, GOCC_CELL_BODY, GOCC_SOMATODENDRITIC_COMPARTMENT

GO Biological Process (6): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), intracellular mRNA localization (GO:0008298), positive regulation of gene expression (GO:0010628), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (6): single-stranded DNA binding (GO:0003697), RNA binding (GO:0003723), mRNA binding (GO:0003729), nucleic acid binding (GO:0003676), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (7): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), ribosome (GO:0005840), membrane (GO:0016020), neuronal cell body (GO:0043025), dendritic shaft (GO:0043198)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
gene expression	2
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
nucleic acid binding	2
binding	2
RNA biosynthetic process	1
RNA localization	1
regulation of gene expression	1
positive regulation of macromolecule biosynthetic process	1
DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
DNA binding	1
RNA binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
somatodendritic compartment	1
cell body	1
dendrite	1

Protein interactions and networks

STRING

1680 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FUBP3	FBP1	P09467	886
FUBP3	HNRNPF	P52597	818
FUBP3	PUF60	Q9UHX1	683
FUBP3	AIMP2	Q13155	551
FUBP3	MYC	P01106	507
FUBP3	PARN	O95453	497
FUBP3	IMP3	Q9NV31	495
FUBP3	KHDC4	Q7Z7F0	473
FUBP3	HNRNPM	P52272	458
FUBP3	XRN2	Q9H0D6	458
FUBP3	CPZ	Q66K79	445
FUBP3	HNRNPK	P61978	441
FUBP3	MATR3	P43243	433
FUBP3	TMEM64	Q6YI46	427
FUBP3	RRM1	P23921	424

IntAct

137 interactions, top by confidence:

A	B	Type	Score
GDI1	RAB4A	psi-mi:“MI:0914”(association)	0.820
FUBP3	QKI	psi-mi:“MI:0915”(physical association)	0.740
QKI	FUBP3	psi-mi:“MI:0915”(physical association)	0.740
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SAV1	SEC16A	psi-mi:“MI:2364”(proximity)	0.570
CDK18	UBL4A	psi-mi:“MI:0914”(association)	0.530
FOXP3	FOXP2	psi-mi:“MI:0914”(association)	0.530
BCOR	CBX4	psi-mi:“MI:0914”(association)	0.530
PAX9	FUBP3	psi-mi:“MI:0915”(physical association)	0.520
FMR1	ACOT7	psi-mi:“MI:0914”(association)	0.500
KIF1C	KIF1B	psi-mi:“MI:2364”(proximity)	0.480
steC	SCD	psi-mi:“MI:0914”(association)	0.460
FUBP3	GRB2	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
FUBP3	ORF20	psi-mi:“MI:0915”(physical association)	0.400
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
FUBP3	E7	psi-mi:“MI:0915”(physical association)	0.370
FUBP3	QKI	psi-mi:“MI:0915”(physical association)	0.370
SSX1	FUBP3	psi-mi:“MI:0915”(physical association)	0.370
XBP1	FUBP3	psi-mi:“MI:0915”(physical association)	0.370
ATXN1	FUBP3	psi-mi:“MI:0915”(physical association)	0.370
OTUB1	EPM2A	psi-mi:“MI:0914”(association)	0.350
Akap8	MATR3	psi-mi:“MI:0914”(association)	0.350
MATR3	BCLAF3	psi-mi:“MI:0914”(association)	0.350
HNRNPA1	MATR3	psi-mi:“MI:0914”(association)	0.350
SEC16A	NCOR2	psi-mi:“MI:0914”(association)	0.350
KIF21B		psi-mi:“MI:0914”(association)	0.350
RHOA	SYNPO2	psi-mi:“MI:0914”(association)	0.350

BioGRID (405): QKI (Two-hybrid), FUBP3 (Affinity Capture-MS), FUBP3 (Affinity Capture-MS), FUBP3 (Affinity Capture-MS), FUBP3 (Affinity Capture-MS), FUBP3 (Affinity Capture-MS), FUBP3 (Affinity Capture-MS), CTSD (Co-fractionation), FUBP3 (Co-fractionation), FUBP3 (Co-fractionation), FUBP3 (Co-fractionation), FUBP3 (Co-fractionation), FUBP3 (Co-fractionation), NDUFS4 (Co-fractionation), NQO1 (Co-fractionation)

ESM2 similar proteins: A0A1W2P872, A1L1C7, A4IIM2, B2RYD2, F1LQ48, O57406, O88532, O95319, P14866, P28659, P51513, P57723, P57724, Q28HE9, Q2PFW9, Q32PX7, Q3U0V1, Q3US41, Q4QQT3, Q4R535, Q58A45, Q5F3T7, Q5NVC8, Q5R8Y8, Q5R995, Q5U231, Q640Q5, Q6DGV1, Q6GPM1, Q6NXG1, Q6P0B1, Q6PF35, Q792H5, Q7T2T1, Q7TSY6, Q7ZXE2, Q80WA4, Q8R081, Q8UVD9, Q91WJ8

Diamond homologs: A0A0B4KGY6, A0A1W2P872, O19048, O19049, O73932, O74919, P51513, P57721, P57722, P60335, P61978, P61979, P61980, Q15365, Q15366, Q2PFW9, Q32PX7, Q3T0D0, Q4R4M6, Q5E9A3, Q5R5H8, Q5RB68, Q5SF07, Q5ZIQ3, Q5ZLP8, Q61990, Q80WA4, Q8UVD9, Q91WJ8, Q96AE4, Q96I24, Q9JKN6, Q9LZ82, Q9SZH4, Q9UNW9, Q9Y6M1, F4KDN0, Q3U0V1, Q86XN8, Q92945

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 158 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
mRNA 3’-end processing	7	13.2×	6e-04
mRNA Polyadenylation	9	7.6×	6e-04
Processing of Capped Intron-Containing Pre-mRNA	8	6.3×	5e-03
Dengue Virus-Host Interactions	12	5.3×	6e-04
mRNA Splicing - Major Pathway	10	5.2×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
mRNA stabilization	6	16.0×	6e-04
negative regulation of translation	10	14.3×	2e-06
mRNA transport	7	13.4×	5e-04
anatomical structure morphogenesis	8	8.1×	1e-03
mRNA processing	11	6.3×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	64
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3651 predictions. Top by Δscore:

Variant	Effect	Δscore
9:130579762:CAGG:C	donor_loss	1.0000
9:130579764:GGT:G	donor_loss	1.0000
9:130579765:GT:G	donor_loss	1.0000
9:130579766:T:A	donor_loss	1.0000
9:130595586:GAGGT:G	donor_loss	1.0000
9:130595589:GTAA:G	donor_loss	1.0000
9:130595590:T:A	donor_loss	1.0000
9:130612504:TA:T	donor_gain	1.0000
9:130612506:G:GG	donor_gain	1.0000
9:130612951:TTCA:T	acceptor_loss	1.0000
9:130612952:TCA:T	acceptor_loss	1.0000
9:130612953:CA:C	acceptor_loss	1.0000
9:130612954:A:AG	acceptor_gain	1.0000
9:130612955:G:GA	acceptor_gain	1.0000
9:130612955:GT:G	acceptor_gain	1.0000
9:130612955:GTT:G	acceptor_gain	1.0000
9:130613023:TTCAG:T	donor_loss	1.0000
9:130613024:TCAGG:T	donor_loss	1.0000
9:130613025:CAGGT:C	donor_loss	1.0000
9:130613026:AGGT:A	donor_loss	1.0000
9:130613027:GGTA:G	donor_loss	1.0000
9:130613029:T:A	donor_loss	1.0000
9:130614287:GAGA:G	acceptor_gain	1.0000
9:130614344:GA:G	donor_gain	1.0000
9:130614346:G:GG	donor_gain	1.0000
9:130617792:CACAG:C	acceptor_loss	1.0000
9:130617794:CAG:C	acceptor_loss	1.0000
9:130617795:A:AG	acceptor_gain	1.0000
9:130617795:AG:A	acceptor_gain	1.0000
9:130617796:G:GG	acceptor_gain	1.0000

AlphaMissense

3764 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:130612497:T:A	V89D	1.000
9:130612499:G:A	G90R	1.000
9:130612499:G:C	G90R	1.000
9:130612500:G:A	G90E	1.000
9:130612956:T:A	I92N	1.000
9:130612959:T:A	I93N	1.000
9:130612961:G:C	G94R	1.000
9:130612962:G:A	G94D	1.000
9:130612962:G:T	G94V	1.000
9:130612971:G:A	G97D	1.000
9:130612980:T:A	I100N	1.000
9:130612980:T:G	I100S	1.000
9:130612992:A:C	Q104P	1.000
9:130613000:T:C	S107P	1.000
9:130613006:T:C	C109R	1.000
9:130613007:G:A	C109Y	1.000
9:130613008:C:G	C109W	1.000
9:130613013:T:A	I111N	1.000
9:130613013:T:G	I111S	1.000
9:130614309:G:C	R123T	1.000
9:130614309:G:T	R123M	1.000
9:130614310:G:C	R123S	1.000
9:130614310:G:T	R123S	1.000
9:130614314:T:C	C125R	1.000
9:130614316:T:G	C125W	1.000
9:130614321:T:A	L127H	1.000
9:130614321:T:C	L127P	1.000
9:130614321:T:G	L127R	1.000
9:130614326:G:A	G129R	1.000
9:130614326:G:C	G129R	1.000

dbSNP variants (sampled 300 via entrez): RS1000006511 (9:130621920 A>G), RS1000007291 (9:130629444 G>A), RS1000022754 (9:130634645 T>C,G), RS1000027999 (9:130589216 T>C), RS1000045265 (9:130595664 C>G), RS1000065954 (9:130627641 G>A,T), RS1000074901 (9:130620606 G>T), RS1000080239 (9:130629627 A>G), RS1000150022 (9:130589375 G>A), RS1000173522 (9:130616432 A>G), RS1000189687 (9:130601190 G>A), RS1000203257 (9:130605419 C>T), RS1000220033 (9:130611248 G>A), RS1000269669 (9:130607577 CATCTGCCTCCTTAGTGTG>C), RS1000275303 (9:130605781 T>C,G)

Disease associations

OMIM: gene MIM:603536 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST000176_5	Height	8.000000e-07
GCST000817_177	Height	3.000000e-17
GCST001956_30	Height	2.000000e-10
GCST002492_4	Bone mineral density (paediatric, lower limb)	5.000000e-06
GCST002492_5	Bone mineral density (paediatric, lower limb)	2.000000e-08
GCST002494_4	Bone mineral density (paediatric, total body less head)	3.000000e-08
GCST002647_33	Height	1.000000e-27
GCST005795_28	Femoral neck bone mineral density	2.000000e-08
GCST006423_9	Fracture	5.000000e-19
GCST007485_7	Anthropometric traits	2.000000e-29
GCST007490_18	Anthropometric traits (multi-trait analysis)	6.000000e-17
GCST007691_16	Femoral neck bone mineral density	3.000000e-22
GCST008059_227	Estimated glomerular filtration rate	5.000000e-07
GCST008163_208	Height	2.000000e-07
GCST008839_9	Height	8.000000e-28
GCST90000025_382	Appendicular lean mass	1.000000e-13
GCST90011900_210	Serum alkaline phosphatase levels	2.000000e-11

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007785	femoral neck bone mineral density
EFO:0004324	body weights and measures
EFO:0004980	appendicular lean mass
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067301 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.51	Kd	3073	nM	CHEMBL5653589
5.51	ED50	3073	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 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
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148403: Binding affinity to human FUBP3 incubated for 45 mins by Kinobead based pull down assay	kd	3.0731	uM

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tretinoin	decreases expression	2
Valproic Acid	decreases expression, decreases methylation	2
TAK-243	decreases sumoylation	1
urushiol	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	increases expression	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	increases secretion, affects cotreatment	1
bisphenol B	increases expression	1
bromovanin	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Dactinomycin	increases secretion, affects cotreatment	1
Doxorubicin	affects expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	decreases phosphorylation	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	affects expression	1
Aflatoxin B1	increases methylation	1
Particulate Matter	decreases expression, increases abundance	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651445	Binding	Binding affinity to human FUBP3 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

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1XV	HAP1 FUBP3 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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