BTF3L4

Summary

BTF3L4 (basic transcription factor 3 like 4, HGNC:30547) is a protein-coding gene on chromosome 1p32.3, encoding Transcription factor BTF3 homolog 4 (Q96K17). It is a selective cancer dependency (DepMap: 61.0% of cell lines).

At a glance

• Clinical variants (ClinVar): 30 total
• Cancer dependency (DepMap): dependent in 61.0% of screened cell lines
• MANE Select transcript: NM_152265

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30547
Approved symbol	BTF3L4
Name	basic transcription factor 3 like 4
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC23908
Ensembl gene	ENSG00000134717
Ensembl biotype	protein_coding
Entrez	91408

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000313334, ENST00000472944, ENST00000477828, ENST00000484036, ENST00000489308, ENST00000524414, ENST00000526132, ENST00000533836, ENST00000878998, ENST00000878999, ENST00000912129, ENST00000912130, ENST00000912131, ENST00000912132, ENST00000960919

RefSeq mRNA: 3 — MANE Select: NM_152265 NM_001136497, NM_001243767, NM_152265

CCDS: CCDS30713, CCDS44146, CCDS58001

Canonical transcript exons

ENST00000313334 — 6 exons

Exon	Start	End
ENSE00001455638	52086712	52090716
ENSE00001836080	52056295	52056379
ENSE00003487256	52059835	52059901
ENSE00003514824	52064825	52064938
ENSE00003557763	52083340	52083541
ENSE00003562757	52086112	52086171

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 98.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.8671 / max 631.5590, expressed in 1793 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2862	16.5244	1773
2861	3.3101	1613
2860	0.0325	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	98.33	gold quality
ganglionic eminence	UBERON:0004023	98.05	gold quality
embryo	UBERON:0000922	98.04	gold quality
tibialis anterior	UBERON:0001385	97.84	gold quality
ventricular zone	UBERON:0003053	97.23	gold quality
monocyte	CL:0000576	96.64	gold quality
deltoid	UBERON:0001476	96.55	gold quality
adrenal tissue	UBERON:0018303	96.53	gold quality
islet of Langerhans	UBERON:0000006	96.51	gold quality
leukocyte	CL:0000738	96.25	gold quality
colonic epithelium	UBERON:0000397	95.96	gold quality
right adrenal gland cortex	UBERON:0035827	95.38	gold quality
right adrenal gland	UBERON:0001233	94.97	gold quality
gastrocnemius	UBERON:0001388	94.93	gold quality
left adrenal gland	UBERON:0001234	94.90	gold quality
muscle of leg	UBERON:0001383	94.87	gold quality
skeletal muscle organ	UBERON:0014892	94.76	gold quality
left adrenal gland cortex	UBERON:0035825	94.71	gold quality
prefrontal cortex	UBERON:0000451	94.65	gold quality
adrenal gland	UBERON:0002369	94.51	gold quality
quadriceps femoris	UBERON:0001377	94.48	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.48	gold quality
pancreas	UBERON:0001264	94.39	gold quality
skeletal muscle tissue	UBERON:0001134	94.34	gold quality
calcaneal tendon	UBERON:0003701	94.34	gold quality
vastus lateralis	UBERON:0001379	94.25	gold quality
smooth muscle tissue	UBERON:0001135	94.24	gold quality
biceps brachii	UBERON:0001507	94.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	94.11	gold quality
body of pancreas	UBERON:0001150	94.09	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

233 targeting BTF3L4, 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-3163	100.00	77.23	8605
HSA-MIR-656-3P	100.00	72.15	2788
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3173-3P	99.98	66.49	1217

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 61.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• Basic Transcription Factor 3 Like 4 Enhances Malignant Phenotypes through Modulating Tumor Cell Function and Immune Microenvironment in Glioma. (PMID:38320629)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	btf3l4	ENSDARG00000089681
mus_musculus	Btf3l4b	ENSMUSG00000114133
rattus_norvegicus	Btf3l4	ENSRNOG00000008512
drosophila_melanogaster	bic	FBGN0000181
drosophila_melanogaster	uncNacbeta	FBGN0031264

Paralogs (3): TAB2 (ENSG00000055208), BTF3 (ENSG00000145741), TAB3 (ENSG00000157625)

Protein

Protein identifiers

Transcription factor BTF3 homolog 4 — Q96K17 (reviewed: Q96K17)

Alternative names: Basic transcription factor 3-like 4

All UniProt accessions (3): E9PL10, E9PPC3, Q96K17

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NAC-beta family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96K17-1	1	yes
Q96K17-2	2
Q96K17-3	3

RefSeq proteins (3): NP_001129969, NP_001230696, NP_689478* (*=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 (9 total): splice variant 3, modified residue 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96K17-F1	77.77	0.39

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 (2): 5, 111

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 172 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, TGCACTT_MIR519C_MIR519B_MIR519A, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, TTTGCAC_MIR19A_MIR19B, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GEORGES_TARGETS_OF_MIR192_AND_MIR215, CAGTATT_MIR200B_MIR200C_MIR429, GCAAGAC_MIR431, BRUINS_UVC_RESPONSE_LATE, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, RATTENBACHER_BOUND_BY_CELF1, PECE_MAMMARY_STEM_CELL_DN

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

1688 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BTF3L4	MAPK1IP1L	Q8NDC0	423
BTF3L4	TCP11L1	Q9NUJ3	402
BTF3L4	MAP7D2	Q96T17	393
BTF3L4	CNOT10	Q9H9A5	387
BTF3L4	GTF2H3	Q13889	385
BTF3L4	THAP6	Q8TBB0	377
BTF3L4	SMYD1	Q8NB12	376
BTF3L4	MYZAP	P0CAP1	368
BTF3L4	SPAG8	Q99932	366
BTF3L4	TXNL1	O43396	363
BTF3L4	GTF2H1	P32780	363
BTF3L4	GALK2	Q01415	359
BTF3L4	C2CD4C	Q8TF44	351
BTF3L4	MAF1	Q9H063	348
BTF3L4	PTER	Q96BW5	340

IntAct

61 interactions, top by confidence:

A	B	Type	Score
MED17	MED19	psi-mi:“MI:0914”(association)	0.840
BTF3L4	TXLNA	psi-mi:“MI:0915”(physical association)	0.780
TXLNA	BTF3L4	psi-mi:“MI:0915”(physical association)	0.780
BTF3L4	TXLNA	psi-mi:“MI:0914”(association)	0.780
GATAD2A	CDK2AP1	psi-mi:“MI:0914”(association)	0.730
BTF3L4	TXLNB	psi-mi:“MI:0915”(physical association)	0.560
BTF3L4	SMYD2	psi-mi:“MI:0915”(physical association)	0.560
SLC25A41	NUDT19	psi-mi:“MI:0914”(association)	0.530
ATP6V0A1	ATP6AP2	psi-mi:“MI:0914”(association)	0.530
BTF3L4	PRIM1	psi-mi:“MI:0914”(association)	0.530
NCBP3	RSL1D1	psi-mi:“MI:0914”(association)	0.350
APP	ESYT2	psi-mi:“MI:0914”(association)	0.350
PB2	DNAJB6	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
CSNK2A1	RPS3A	psi-mi:“MI:0914”(association)	0.350
PSPC1	MCRIP1	psi-mi:“MI:0914”(association)	0.350
RPS16	MCRIP1	psi-mi:“MI:0914”(association)	0.350
FGB	KIF2A	psi-mi:“MI:0914”(association)	0.350
BTF3L4	NACAD	psi-mi:“MI:0914”(association)	0.350
NTNG1	UBA6	psi-mi:“MI:0914”(association)	0.350
BBS1	SHTN1	psi-mi:“MI:0914”(association)	0.350
DOK4	SHTN1	psi-mi:“MI:0914”(association)	0.350
AHR	SHTN1	psi-mi:“MI:0914”(association)	0.350
ANKRD49	SHTN1	psi-mi:“MI:0914”(association)	0.350
ZBTB2	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (125): TXLNB (Two-hybrid), TXLNA (Two-hybrid), BTF3L4 (Reconstituted Complex), BTF3L4 (Affinity Capture-MS), BTF3 (Co-fractionation), HNRNPU (Co-fractionation), NACA (Co-fractionation), BTF3L4 (Proximity Label-MS), BTF3L4 (Affinity Capture-MS), BTF3L4 (Affinity Capture-MS), BTF3L4 (Affinity Capture-RNA), BTF3L4 (Affinity Capture-MS), BTF3L4 (Proximity Label-MS), BTF3L4 (Proximity Label-MS), BTF3L4 (Proximity Label-MS)

ESM2 similar proteins: A1CMP1, A2R091, A3GHR2, A4RC23, A5DF06, A5DT59, A5FVX2, A6R5Z3, A6S6B0, A6ZWL1, A7F9B8, A9VYZ2, B7KVD3, P20290, P27499, Q02642, Q08454, Q0CGL5, Q0ULD0, Q18885, Q1DI23, Q1MJ60, Q2H4X9, Q2KAE9, Q2KIY7, Q3V4Q3, Q4I283, Q4KLF5, Q4P9Y9, Q54TR8, Q59TU0, Q5ASI4, Q5M8V0, Q5RC59, Q5ZJG3, Q64152, Q6BLV1, Q6C2F3, Q6CR46, Q6FKD1

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

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	13
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

720 predictions. Top by Δscore:

Variant	Effect	Δscore
1:52056376:TCAGG:T	donor_loss	1.0000
1:52056377:CAGGT:C	donor_loss	1.0000
1:52056378:AGGTG:A	donor_loss	1.0000
1:52056379:GGT:G	donor_loss	1.0000
1:52056380:G:GA	donor_loss	1.0000
1:52056381:T:G	donor_loss	1.0000
1:52059830:CCTA:C	acceptor_loss	1.0000
1:52059831:CTA:C	acceptor_loss	1.0000
1:52059832:TAG:T	acceptor_loss	1.0000
1:52059833:A:AG	acceptor_gain	1.0000
1:52059833:A:AT	acceptor_loss	1.0000
1:52059834:G:GG	acceptor_gain	1.0000
1:52064820:TTCA:T	acceptor_loss	1.0000
1:52064822:CA:C	acceptor_loss	1.0000
1:52064823:A:AC	acceptor_loss	1.0000
1:52064823:A:AG	acceptor_gain	1.0000
1:52064823:AG:A	acceptor_gain	1.0000
1:52064823:AGG:A	acceptor_gain	1.0000
1:52064824:G:GC	acceptor_gain	1.0000
1:52064824:GG:G	acceptor_gain	1.0000
1:52064824:GGG:G	acceptor_gain	1.0000
1:52064824:GGGT:G	acceptor_gain	1.0000
1:52064824:GGGTA:G	acceptor_gain	1.0000
1:52064936:GAG:G	donor_gain	1.0000
1:52064937:AGGTA:A	donor_loss	1.0000
1:52083337:CA:C	acceptor_loss	1.0000
1:52083338:AGG:A	acceptor_loss	1.0000
1:52083339:GGT:G	acceptor_gain	1.0000
1:52083537:GCAAG:G	donor_gain	1.0000
1:52083539:AAGG:A	donor_loss	1.0000

AlphaMissense

1054 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:52059894:G:A	G16E	1.000
1:52064825:G:C	G19R	1.000
1:52064826:G:A	G19D	1.000
1:52064834:C:A	R22S	1.000
1:52064838:G:C	R23T	1.000
1:52064839:A:C	R23S	1.000
1:52064839:A:T	R23S	1.000
1:52064855:C:G	H29D	1.000
1:52064886:T:A	L39H	1.000
1:52064886:T:C	L39P	1.000
1:52064898:T:C	L43P	1.000
1:52064922:T:A	I51K	1.000
1:52064931:T:A	I54N	1.000
1:52064931:T:G	I54S	1.000
1:52083341:T:A	V57E	1.000
1:52083345:C:A	N58K	1.000
1:52083345:C:G	N58K	1.000
1:52083368:T:A	V66D	1.000
1:52083376:T:C	F69L	1.000
1:52083377:T:C	F69S	1.000
1:52083378:C:A	F69L	1.000
1:52083378:C:G	F69L	1.000
1:52083386:C:A	P72H	1.000
1:52083386:C:G	P72R	1.000
1:52083392:T:A	V74D	1.000
1:52083395:A:C	Q75P	1.000
1:52083397:G:C	A76P	1.000
1:52083398:C:A	A76D	1.000
1:52083400:T:C	S77P	1.000
1:52083418:T:C	F83L	1.000

dbSNP variants (sampled 300 via entrez): RS1000121926 (1:52075666 T>A), RS1000206401 (1:52056239 G>C), RS1000217244 (1:52065599 A>C,G), RS1000285150 (1:52069488 A>G), RS1000305585 (1:52075837 G>A), RS1000322937 (1:52056435 C>A,T), RS1000398724 (1:52078466 G>T), RS1000484154 (1:52084040 A>G), RS1000614527 (1:52071515 T>C), RS1000658128 (1:52057530 T>C), RS1000819281 (1:52064061 G>T), RS1000854392 (1:52071601 T>C,G), RS1000902898 (1:52090268 T>C), RS1000916156 (1:52064499 A>G), RS1000948287 (1:52091008 G>C,T)

Disease associations

OMIM: gene `` | 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: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression, increases expression	2
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
beauvericin	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	affects expression	1
arsenite	affects binding, increases reaction	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
enniatins	affects cotreatment, decreases expression	1
nutlin 3	affects cotreatment, increases secretion	1
jinfukang	decreases expression	1
bisphenol AF	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Dactinomycin	affects cotreatment, increases secretion	1
Ivermectin	decreases expression	1
Ozone	affects expression, increases abundance	1
Quercetin	decreases expression	1
Ribonucleotides	affects binding	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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