BTF3

Summary

BTF3 (basic transcription factor 3, HGNC:1125) is a protein-coding gene on chromosome 5q13.2, encoding Transcription factor BTF3 (P20290). When associated with NACA, prevents inappropriate targeting of non-secretory polypeptides to the endoplasmic reticulum (ER).

This gene encodes the basic transcription factor 3. This protein forms a stable complex with RNA polymerase IIB and is required for transcriptional initiation. Alternative splicing results in multiple transcript variants encoding different isoforms. This gene has multiple pseudogenes.

Source: NCBI Gene 689 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 35 total
• Druggable target: yes
• MANE Select transcript: NM_001037637

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1125
Approved symbol	BTF3
Name	basic transcription factor 3
Location	5q13.2
Locus type	gene with protein product
Status	Approved
Aliases	BTF3a, BTF3b
Ensembl gene	ENSG00000145741
Ensembl biotype	protein_coding
OMIM	602542
Entrez	689

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 retained_intron, 6 protein_coding, 1 nonsense_mediated_decay

ENST00000335895, ENST00000380591, ENST00000507081, ENST00000508901, ENST00000509708, ENST00000510787, ENST00000512257, ENST00000514360, ENST00000514505, ENST00000676856, ENST00000676862, ENST00000677654, ENST00000678135, ENST00000679077

RefSeq mRNA: 4 — MANE Select: NM_001037637 NM_001037637, NM_001207, NM_001393652, NM_001393653

CCDS: CCDS34185, CCDS4019

Canonical transcript exons

ENST00000380591 — 6 exons

Exon	Start	End
ENSE00001182158	73498442	73498799
ENSE00001485570	73505192	73505667
ENSE00003520230	73502916	73503117
ENSE00003575504	73502488	73502601
ENSE00003758849	73499134	73499202
ENSE00003789657	73504347	73504403

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 709.5357 / max 11079.8979, expressed in 1827 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
57042	709.5357	1827

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of sigmoid colon	UBERON:0004993	99.76	gold quality
mammary duct	UBERON:0001765	99.74	gold quality
penis	UBERON:0000989	99.72	gold quality
colonic mucosa	UBERON:0000317	99.71	gold quality
left ovary	UBERON:0002119	99.70	gold quality
embryo	UBERON:0000922	99.69	gold quality
mammalian vulva	UBERON:0000997	99.69	gold quality
ganglionic eminence	UBERON:0004023	99.69	gold quality
oral cavity	UBERON:0000167	99.68	gold quality
ovary	UBERON:0000992	99.68	gold quality
trabecular bone tissue	UBERON:0002483	99.68	gold quality
epithelium of mammary gland	UBERON:0003244	99.67	gold quality
mammary gland	UBERON:0001911	99.66	gold quality
thoracic mammary gland	UBERON:0005200	99.66	gold quality
endometrium	UBERON:0001295	99.65	gold quality
right ovary	UBERON:0002118	99.65	gold quality
cartilage tissue	UBERON:0002418	99.65	gold quality
upper leg skin	UBERON:0004262	99.65	gold quality
zone of skin	UBERON:0000014	99.64	gold quality
skin of abdomen	UBERON:0001416	99.64	gold quality
cauda epididymis	UBERON:0004360	99.64	gold quality
seminal vesicle	UBERON:0000998	99.63	gold quality
skin of leg	UBERON:0001511	99.63	gold quality
caput epididymis	UBERON:0004358	99.63	gold quality
cortical plate	UBERON:0005343	99.63	gold quality
pharyngeal mucosa	UBERON:0000355	99.62	gold quality
jejunal mucosa	UBERON:0000399	99.62	gold quality
skin of hip	UBERON:0001554	99.62	gold quality
superficial temporal artery	UBERON:0001614	99.62	gold quality
adult organism	UBERON:0007023	99.62	gold quality

Single-cell (SCXA)

Detected in 14 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-CURD-122	yes	37.11
E-CURD-88	yes	32.29
E-MTAB-10042	yes	14.28
E-GEOD-130148	yes	7.76
E-CURD-112	yes	5.34
E-CURD-98	no	2496.40
E-HCAD-1	no	2383.04
E-CURD-79	no	2077.58
E-MTAB-8207	no	1460.42
E-HCAD-4	no	103.42
E-CURD-114	no	62.75
E-HCAD-10	no	34.51
E-GEOD-125970	no	18.16
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting BTF3, 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-3163	100.00	77.23	8605
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-3177-5P	99.65	70.38	1174
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-513A-3P	99.39	70.63	3620
HSA-MIR-513C-3P	99.39	70.63	3620
HSA-MIR-3160-5P	99.28	69.07	1938
HSA-MIR-3606-3P	99.11	69.84	3254
HSA-MIR-361-5P	98.95	70.16	1340
HSA-MIR-374A-3P	98.87	67.82	1531
HSA-MIR-219A-2-3P	98.62	68.78	797
HSA-MIR-4274	98.59	66.10	630
HSA-MIR-4511	98.32	67.97	1500
HSA-MIR-4659A-5P	98.03	66.42	819
HSA-MIR-4659B-5P	98.03	66.84	979
HSA-MIR-6529-5P	97.85	66.47	673

Literature-anchored findings (GeneRIF, showing 19)

• BTF3 is overexpressed in pancreatic ductal adenocarcinoma , where it acts as a transcriptional regulator rather than a direct modulator of apoptosis. (PMID:17312387)
• BTF3 interacts with ERalpha that has been activated either by 17beta-estradiol (ligand-dependent activation) or by epidermal growth factor (ligand-independent activation). (PMID:18025262)
• In addition to RNA polymerase II (otherwise RNA pol II, RNA polymerase B), four general transcription factors are required for initiation of transcription: BTF1 (also referred to as TFIID) which has recently been cloned from yeast, BTF2, BTF3 and STF. (PMID:2320128)
• may have a functional role in protecting against caries (PMID:23363935)
• BTF3 overexpression may be an early event in colorectal cancer development and could be useful biomarker for the early stage of colorectal cancers (CRC); BTF3 has positive correlations with NF-kappaB, RAD50, MRE11, NBS1 and AEG-1 and might influence complex signal pathways in CRC (PMID:23532689)
• BTF3 expression is associated with enhanced cell proliferation, reduced cell cycle regulation and apoptosis and its silencing decreased colony forming and proliferation of gastric cancer cells. (PMID:23901224)
• BTF3, HINT1, NDRG1 and ODC1 protein over-expression in human prostate cancer tissue (PMID:24386364)
• Findings provide a novel understanding of the mechanism of gastric cancer and highlight the important role of BTF3/FOXM1 in tumor growth and BTF3/JAK2/STAT3 in EMT and metastasis (PMID:28276310)
• TCGA analysis reveals high expression levels of BTF3 in luminal/ER + breast cancer and cell line models harboring ERalpha overexpression. Concordantly, BTF3 expression is highly and strongly associated with ESR1 expression in multiple breast cancer cohorts. (PMID:30315845)
• Study showed that BTF3 is overexpressed in prostate cancer (PCa) tissues and correlates with stem-like traits. Cancer stem-like characteristics in PCa including self-renewal and metastatic potential were impaired by BTF3 loss. BTF3 could stabilize BMI1, a crucial regulator of prostate stem cell self-renewal. More importantly, data revealed that BTF3 is highly predictive of poor prognosis. (PMID:31138311)
• BTF3 is positively related to CRC and BTF3-siRNA attenuated the tumorigenicity of colorectal cancer cells via MAD2L2, MCM3 and PLK1 activity reduction. (PMID:31263147)
• Expression of BTF3 is upregulated in hypopharyngeal squamous cell carcinoma and this upregulation is positively correlated with lymph node metastasis of this malignancy. (PMID:31404775)
• miR802 inhibits the epithelialmesenchymal transition, migration and invasion of cervical cancer by regulating BTF3. (PMID:32582971)
• BTF3 promotes stemness and inhibits TypeInterferon signaling pathway in triple-negative breast cancer. (PMID:33383560)
• BTF3 confers oncogenic activity in prostate cancer through transcriptional upregulation of Replication Factor C. (PMID:33414468)
• BTF3-mediated regulation of BMI1 promotes colorectal cancer through influencing epithelial-mesenchymal transition and stem cell-like traits. (PMID:34293363)
• BTF3 promotes proliferation and glycolysis in hepatocellular carcinoma by regulating GLUT1. (PMID:37382415)
• Ubiquitination-specific protease 7 enhances stemness of hepatocellular carcinoma by stabilizing basic transcription factor 3. (PMID:38340226)
• METTL3-driven m6A modification of lncRNA FAM230B suppresses ferroptosis by modulating miR-27a-5p/BTF3 axis in gastric cancer. (PMID:39278369)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Btf3	ENSMUSG00000021660
rattus_norvegicus	Btf3	ENSRNOG00000016912
caenorhabditis_elegans		WBGENE00002045

Paralogs (3): TAB2 (ENSG00000055208), BTF3L4 (ENSG00000134717), TAB3 (ENSG00000157625)

Protein

Protein identifiers

Transcription factor BTF3 — P20290 (reviewed: P20290)

Alternative names: Nascent polypeptide-associated complex subunit beta, RNA polymerase B transcription factor 3

All UniProt accessions (6): A0A7I2V3T6, A0A7I2V5Y3, A0A7I2YQL2, D6RDG3, H0Y9Y1, P20290

UniProt curated annotations — full annotation on UniProt →

Function. When associated with NACA, prevents inappropriate targeting of non-secretory polypeptides to the endoplasmic reticulum (ER). Binds to nascent polypeptide chains as they emerge from the ribosome and blocks their interaction with the signal recognition particle (SRP), which normally targets nascent secretory peptides to the ER. BTF3 is also a general transcription factor that can form a stable complex with RNA polymerase II. Required for the initiation of transcription.

Subunit / interactions. Part of the nascent polypeptide-associated complex (NAC), which is a heterodimer of NACA and BTF3 (via NAC-A/B domains). NAC associates with ribosomes through the BTF3/NACB subunit. Both subunits can contact nascent polypeptide chains.

Subcellular location. Cytoplasm. Nucleus.

Similarity. Belongs to the NAC-beta family.

Isoforms (2)

UniProt ID	Names	Canonical?
P20290-1	1, BTF3a	yes
P20290-2	2, BTF3b

RefSeq proteins (4): NP_001032726, NP_001198, NP_001380581, NP_001380582 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002715	Nas_poly-pep-assoc_cplx_dom	Domain
IPR038187	NAC_A/B_dom_sf	Homologous_superfamily
IPR039370	BTF3	Family

Pfam: PF01849

UniProt features (25 total): modified residue 6, strand 5, sequence conflict 4, helix 3, region of interest 2, chain 1, domain 1, splice variant 1, turn 1, compositionally biased region 1

Structure

Experimental structures (PDB)

52 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
3MCB	X-RAY DIFFRACTION	1.9
9I2D	ELECTRON MICROSCOPY	2.19
9PBE	ELECTRON MICROSCOPY	2.19
9S3D	ELECTRON MICROSCOPY	2.32
9S3B	ELECTRON MICROSCOPY	2.38
9S3C	ELECTRON MICROSCOPY	2.42
9QLO	ELECTRON MICROSCOPY	2.47
9P8B	ELECTRON MICROSCOPY	2.48
3LKX	X-RAY DIFFRACTION	2.5
9P7D	ELECTRON MICROSCOPY	2.57
9QLQ	ELECTRON MICROSCOPY	2.57
9P7E	ELECTRON MICROSCOPY	2.59
9MR4	ELECTRON MICROSCOPY	2.65
9P7O	ELECTRON MICROSCOPY	2.65
9P73	ELECTRON MICROSCOPY	2.66
9PA7	ELECTRON MICROSCOPY	2.67
9P7Y	ELECTRON MICROSCOPY	2.75
9QLP	ELECTRON MICROSCOPY	2.75
9P9I	ELECTRON MICROSCOPY	2.77
9P7C	ELECTRON MICROSCOPY	2.78
9P72	ELECTRON MICROSCOPY	2.8
9P7K	ELECTRON MICROSCOPY	2.8
9QQA	ELECTRON MICROSCOPY	2.8
9P7A	ELECTRON MICROSCOPY	2.81
9NDP	ELECTRON MICROSCOPY	2.82
7QWQ	ELECTRON MICROSCOPY	2.83
9P76	ELECTRON MICROSCOPY	2.83
9P7N	ELECTRON MICROSCOPY	2.83
9P7X	ELECTRON MICROSCOPY	2.83
9P9H	ELECTRON MICROSCOPY	2.84

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P20290-F1	73.08	0.28

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 (6): 173, 19, 30, 46, 54, 160

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9918487	Dengue Virus Genome Translation and Replication

MSigDB gene sets: 216 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, WANG_CLIM2_TARGETS_UP, MODULE_151, ENK_UV_RESPONSE_KERATINOCYTE_UP, MORF_UBE2I, MORF_HDAC1, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, ACTGCAG_MIR173P, YY1_Q6, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_LOCALIZATION, PUJANA_CHEK2_PCC_NETWORK, GOBP_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM, MORF_SKP1A, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, MORF_CCNI

GO Biological Process (3): in utero embryonic development (GO:0001701), protein transport (GO:0015031), negative regulation of protein localization to endoplasmic reticulum (GO:1905551)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), nascent polypeptide-associated complex (GO:0005854)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Dengue Virus Infection	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cytoplasm	2
chordate embryonic development	1
transport	1
intracellular protein localization	1
establishment of protein localization	1
protein localization to endoplasmic reticulum	1
negative regulation of protein localization	1
regulation of protein localization to endoplasmic reticulum	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
protein-containing complex	1

Protein interactions and networks

STRING

2901 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BTF3	CLN5	O75503	810
BTF3	RPL31	P12947	717
BTF3	A0A3B3ITS8	A0A3B3ITS8	581
BTF3	GJA1	P17302	489
BTF3	DNAJC2	Q99543	465
BTF3	CCNL2	Q96S94	425
BTF3	TAF15	Q92804	414
BTF3	CILK1	Q9UPZ9	407
BTF3	POMC	P01189	380
BTF3	KAT7	O95251	370
BTF3	TNF	P01375	370
BTF3	ELOA	Q14241	365
BTF3	MYOM2	P54296	362
BTF3	BCCIP	Q9P287	362
BTF3	PEX6	Q13608	347
BTF3	OFD1	O75665	347

IntAct

70 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
TXLNA	BTF3	psi-mi:“MI:0915”(physical association)	0.670
BTF3	TXLNA	psi-mi:“MI:0915”(physical association)	0.670
TXLNB	BTF3	psi-mi:“MI:0915”(physical association)	0.560
BTF3	TXLNB	psi-mi:“MI:0915”(physical association)	0.560
IFTAP	BTF3	psi-mi:“MI:0915”(physical association)	0.510
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
rep	BTF3	psi-mi:“MI:0915”(physical association)	0.370
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
CEP43	CCHCR1	psi-mi:“MI:0914”(association)	0.350
CSNK2A2	WDR46	psi-mi:“MI:0914”(association)	0.350
SMC6	IFT88	psi-mi:“MI:0914”(association)	0.350
RPL10	RPS6	psi-mi:“MI:0914”(association)	0.350
Aff1	UVRAG	psi-mi:“MI:0914”(association)	0.350
Zbtb48	VWA8	psi-mi:“MI:0914”(association)	0.350
Mus81	KIF1B	psi-mi:“MI:0914”(association)	0.350
BFRF1A	SHTN1	psi-mi:“MI:0914”(association)	0.350
HIF1AN	CNOT1	psi-mi:“MI:0914”(association)	0.350
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
APP	ESYT2	psi-mi:“MI:0914”(association)	0.350
C9orf72	CHD2	psi-mi:“MI:0914”(association)	0.350
VAMP5	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (908): BTF3 (Reconstituted Complex), TXLNB (Two-hybrid), TXLNA (Two-hybrid), BTF3 (Two-hybrid), BTF3 (Co-fractionation), BTF3 (Co-fractionation), NACA (Co-fractionation), NACA2 (Co-fractionation), SRSF2 (Co-fractionation), BTF3 (Affinity Capture-MS), BTF3 (Proximity Label-MS), BTF3 (Proximity Label-MS), BTF3 (Proximity Label-MS), BTF3 (Proximity Label-MS), BTF3 (Proximity Label-MS)

ESM2 similar proteins: A0A0D1CVX2, A0A0D1E6R6, A0A1D1V3Z0, A5HBE1, B5YWI0, B6KEU8, B6KJ32, B7UM99, C6UYL8, D1FQ14, D3QW22, G5EHI7, K9N4Q4, O00834, O00933, O46203, O75956, O84462, P03093, P03095, P05686, P06651, P0C9Z8, P0DJ90, P0DJ91, P0DJ92, P0DOJ1, P0DOJ2, P0DOJ3, P20290, P23117, P23118, P24608, P35939, P90661, Q06428, Q27002, Q27003, Q2KEJ2, Q3L6L8

Diamond homologs: A1CMP1, A1DL98, A2R091, A3GHR2, A4RC23, A5DF06, A5DT59, A6R5Z3, A6S6B0, A6ZWL1, A6ZYK4, A7F9B8, P0CP08, P0CP09, P20290, P40314, Q02642, Q0CGL5, Q0ULD0, Q18885, Q1DI23, Q2H4X9, Q2KIY7, Q2U6N1, Q4I283, Q4KLF5, Q4P9Y9, Q4WCX4, Q54TR8, Q59TU0, Q5ASI4, Q5M8V0, Q5RC59, Q5ZJG3, Q64152, Q6BLV1, Q6C2F3, Q6CR46, Q6FKD1, Q6PC91

SIGNOR signaling

10 interactions.

A	Effect	B	Mechanism
BTF3	“up-regulates quantity by expression”	HPSE2	“transcriptional regulation”
BTF3	“down-regulates quantity by repression”	RRAS2	“transcriptional regulation”
BTF3	“down-regulates quantity by repression”	MADCAM1	“transcriptional regulation”
BTF3	“down-regulates quantity by repression”	IRAG1	“transcriptional regulation”
BTF3	“up-regulates quantity by expression”	ABL2	“transcriptional regulation”
BTF3	“up-regulates quantity by expression”	ATM	“transcriptional regulation”
BTF3	“up-regulates quantity by expression”	EPHB2	“transcriptional regulation”
BTF3	“down-regulates quantity by repression”	NFKB1	“transcriptional regulation”
BTF3	“down-regulates quantity by repression”	SSPN	“transcriptional regulation”
IFTAP	“down-regulates activity”	BTF3	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 84 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
Loss of Nlp from mitotic centrosomes	6	17.3×	2e-04
Loss of proteins required for interphase microtubule organization from the centrosome	6	17.3×	2e-04
AURKA Activation by TPX2	6	16.6×	2e-04
Recruitment of mitotic centrosome proteins and complexes	6	14.8×	4e-04
Regulation of PLK1 Activity at G2/M Transition	6	13.8×	4e-04
Recruitment of NuMA to mitotic centrosomes	6	12.7×	6e-04
Anchoring of the basal body to the plasma membrane	6	12.3×	6e-04

GO biological processes:

GO term	Partners	Fold	FDR
non-motile cilium assembly	6	24.6×	1e-04
cilium assembly	8	8.3×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

726 predictions. Top by Δscore:

Variant	Effect	Δscore
5:73499200:A:T	donor_gain	1.0000
5:73499203:G:GG	donor_gain	1.0000
5:73502479:T:TA	acceptor_gain	1.0000
5:73502484:TTA:T	acceptor_loss	1.0000
5:73502485:TAGG:T	acceptor_loss	1.0000
5:73502486:A:AG	acceptor_gain	1.0000
5:73502486:AG:A	acceptor_gain	1.0000
5:73502486:AGGGA:A	acceptor_loss	1.0000
5:73502487:G:GG	acceptor_gain	1.0000
5:73502487:GG:G	acceptor_gain	1.0000
5:73502487:GGGA:G	acceptor_gain	1.0000
5:73502487:GGGAA:G	acceptor_gain	1.0000
5:73502913:TAGGT:T	acceptor_loss	1.0000
5:73502914:A:AG	acceptor_gain	1.0000
5:73502915:G:GA	acceptor_loss	1.0000
5:73502915:G:GC	acceptor_gain	1.0000
5:73502915:GGT:G	acceptor_gain	1.0000
5:73502915:GGTGA:G	acceptor_gain	1.0000
5:73503113:ACAAT:A	donor_gain	1.0000
5:73503114:CAAT:C	donor_gain	1.0000
5:73503114:CAATG:C	donor_loss	1.0000
5:73503116:AT:A	donor_gain	1.0000
5:73503117:TG:T	donor_loss	1.0000
5:73503118:G:GC	donor_loss	1.0000
5:73503118:G:GG	donor_gain	1.0000
5:73503119:TGAG:T	donor_loss	1.0000
5:73504343:A:AG	acceptor_gain	1.0000
5:73504344:T:G	acceptor_gain	1.0000
5:73504344:TAGCT:T	acceptor_loss	1.0000
5:73504345:A:AG	acceptor_gain	1.0000

AlphaMissense

1335 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:73499195:G:A	G65D	1.000
5:73499198:G:A	G66E	1.000
5:73502488:G:A	G68R	1.000
5:73502488:G:C	G68R	1.000
5:73502489:G:A	G68E	1.000
5:73502497:C:A	R71S	1.000
5:73502501:G:C	R72T	1.000
5:73502502:A:C	R72S	1.000
5:73502502:A:T	R72S	1.000
5:73502505:G:C	K73N	1.000
5:73502505:G:T	K73N	1.000
5:73502518:C:G	H78D	1.000
5:73502536:G:C	D84H	1.000
5:73502539:G:C	D85H	1.000
5:73502543:A:T	K86I	1.000
5:73502544:A:C	K86N	1.000
5:73502544:A:T	K86N	1.000
5:73502549:T:A	L88H	1.000
5:73502549:T:C	L88P	1.000
5:73502561:T:C	L92S	1.000
5:73502585:T:A	I100N	1.000
5:73502585:T:C	I100T	1.000
5:73502585:T:G	I100S	1.000
5:73502594:T:A	I103N	1.000
5:73502594:T:G	I103S	1.000
5:73502599:G:A	E105K	1.000
5:73502917:T:A	V106E	1.000
5:73502921:T:A	N107K	1.000
5:73502921:T:G	N107K	1.000
5:73502923:T:A	M108K	1.000

dbSNP variants (sampled 300 via entrez): RS1000146189 (5:73496851 A>G), RS1000678847 (5:73502434 A>G), RS1000921866 (5:73499703 T>C), RS1001116991 (5:73497827 C>T), RS1001148339 (5:73498289 C>T), RS1001340983 (5:73499816 G>A), RS1001725645 (5:73501638 G>A), RS1001875349 (5:73500206 C>G), RS1002387604 (5:73501374 G>A), RS1002499828 (5:73505544 A>G,T), RS1002920869 (5:73497017 A>G), RS1003658550 (5:73499874 A>G), RS1003801630 (5:73500150 A>G), RS1003815672 (5:73501753 G>A), RS1004177769 (5:73503625 G>A)

Disease associations

OMIM: gene MIM:602542 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066943 (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
6.62	Kd	237.6	nM	CHEMBL5653589
6.62	ED50	237.6	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	2147962: Binding affinity to human BTF3 incubated for 45 mins by Kinobead based pull down assay	kd	0.2376	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
arsenite	affects binding, increases reaction, decreases expression, increases abundance	2
sodium arsenite	decreases expression, increases abundance	2
Tretinoin	affects expression, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
uranyl acetate	affects expression	1
bisphenol A	decreases expression	1
geraniol	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
quinoline	decreases expression	1
diallyl trisulfide	increases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
tamibarotene	affects expression	1
antimonite	decreases expression, increases abundance	1
chloropicrin	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
bisphenol B	increases expression	1
abrine	decreases expression	1
LDN 193189	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Antimony Potassium Tartrate	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases expression	1
Cadmium	decreases expression	1
Caffeine	decreases phosphorylation	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
CHEMBL5651004	Binding	Binding affinity to human BTF3 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.