BEND3

Summary

BEND3 (BEN domain containing 3, HGNC:23040) is a protein-coding gene on chromosome 6q21, encoding BEN domain-containing protein 3 (Q5T5X7). Transcriptional repressor which associates with the NoRC (nucleolar remodeling complex) complex and plays a key role in repressing rDNA transcription.

Enables rDNA binding activity. Involved in negative regulation of macromolecule biosynthetic process; positive regulation of ATP metabolic process; and protein homooligomerization. Located in heterochromatin; nucleolus; and nucleoplasm.

Source: NCBI Gene 57673 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 121 total — 1 pathogenic
• Phenotypes (HPO): 1
• Druggable target: yes
• MANE Select transcript: NM_001367314

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23040
Approved symbol	BEND3
Name	BEN domain containing 3
Location	6q21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000178409
Ensembl biotype	protein_coding
OMIM	616374
Entrez	57673

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 16 protein_coding

ENST00000369042, ENST00000429433, ENST00000905465, ENST00000928358, ENST00000928359, ENST00000928360, ENST00000928361, ENST00000928362, ENST00000928363, ENST00000928364, ENST00000928365, ENST00000928366, ENST00000928367, ENST00000928368, ENST00000928369, ENST00000943403

RefSeq mRNA: 2 — MANE Select: NM_001367314 NM_001080450, NM_001367314

CCDS: CCDS34507

Canonical transcript exons

ENST00000369042 — 4 exons

Exon	Start	End
ENSE00001448687	107065182	107070950
ENSE00001448688	107098551	107098753
ENSE00001448689	107099249	107099296
ENSE00001448690	107115090	107115515

Expression profiles

Bgee: expression breadth ubiquitous, 190 present calls, max score 87.67.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9297 / max 22.2995, expressed in 451 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
74921	0.4560	273
204141	0.2477	117
74920	0.2261	111

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	87.67	gold quality
tibialis anterior	UBERON:0001385	87.02	silver quality
epithelial cell of pancreas	CL:0000083	82.73	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.64	gold quality
pancreatic ductal cell	CL:0002079	81.15	silver quality
nasal cavity epithelium	UBERON:0005384	79.49	gold quality
secondary oocyte	CL:0000655	79.37	gold quality
endothelial cell	CL:0000115	78.18	silver quality
ventricular zone	UBERON:0003053	78.17	gold quality
deltoid	UBERON:0001476	77.38	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.58	gold quality
ganglionic eminence	UBERON:0004023	76.44	gold quality
tibia	UBERON:0000979	76.30	gold quality
cortical plate	UBERON:0005343	75.20	gold quality
oviduct epithelium	UBERON:0004804	74.56	gold quality
colonic mucosa	UBERON:0000317	74.25	gold quality
oocyte	CL:0000023	74.21	gold quality
cauda epididymis	UBERON:0004360	73.99	gold quality
corpus epididymis	UBERON:0004359	73.65	gold quality
mucosa of sigmoid colon	UBERON:0004993	73.64	gold quality
esophagus squamous epithelium	UBERON:0006920	73.64	silver quality
gingival epithelium	UBERON:0001949	72.95	silver quality
gingiva	UBERON:0001828	72.84	silver quality
visceral pleura	UBERON:0002401	72.78	silver quality
germinal epithelium of ovary	UBERON:0001304	72.74	silver quality
buccal mucosa cell	CL:0002336	72.50	gold quality
cartilage tissue	UBERON:0002418	71.95	gold quality
layer of synovial tissue	UBERON:0007616	71.95	gold quality
kidney epithelium	UBERON:0004819	71.86	gold quality
Brodmann (1909) area 23	UBERON:0013554	71.74	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.62

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

• associates with heterochromatin and represses transcription (PMID:21914818)
• Three basic amino acid residues located in the N-terminal region of BEND3 (BEND356-58, KRK) are essential for its nuclear localization, suggesting that these residues play a role as a functional nuclear localization signals. (PMID:25600804)
• Data show that SUMOylated BANP, E5R, and Nac1 (BEN) domain 3 (BEND3) stabilizes NoRC component TTF-1-interacting protein 5 (Tip5)via association with ubiquitin specific protease 21 (USP21) debiquitinase. (PMID:26100909)
• propose that there is a link between binding of BEND3 to the CALR rs138452745 C-allele and removal of NFI binding site from this nucleotide, and the evolution of human-specific higher brain functions (PMID:26481236)
• Data shows that BEND3 associates with chromatin remodeling complexes to modulate gene expression and heterochromatin organization. (PMID:26507581)
• Characterization of the NTPR and BD1 interacting domains of the human PICH-BEND3 complex has been reported. (PMID:27487930)
• Data indicate BEND3 as a new interaction partner for PICH in mitosis, and have defined the residues within a TPR-BEN domain interface that mediate this interaction. (PMID:28977671)
• BEND3 safeguards pluripotency by repressing differentiation-associated genes. (PMID:35217604)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	bend3	ENSDARG00000076903
mus_musculus	Bend3	ENSMUSG00000038214
rattus_norvegicus	Bend3	ENSRNOG00000046505

Protein

Protein identifiers

BEN domain-containing protein 3 — Q5T5X7 (reviewed: Q5T5X7)

All UniProt accessions (1): Q5T5X7

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor which associates with the NoRC (nucleolar remodeling complex) complex and plays a key role in repressing rDNA transcription. The sumoylated form modulates the stability of the NoRC complex component BAZ2A/TIP5 by controlling its USP21-mediated deubiquitination. Binds to unmethylated major satellite DNA and is involved in the recruitment of the Polycomb repressive complex 2 (PRC2) to major satellites. Stimulates the ERCC6L translocase and ATPase activities.

Subunit / interactions. Homooligomer, probably a homooctamer. Interacts with HDAC2 and HDAC3, but not HDAC1. Interacts with SALL4. Interacts with SMARCA5/SNF2H, BAZ2A/TIP5 and USP21. Interacts with the nucleosome remodeling and histone deacetylase (NuRD) repressor complex. Interacts (via BEN domains 1 and 3) with ERCC6L (via N-terminal TPR repeat); the interaction is direct.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Expressed at least in heart, kidney, liver, ovary and spleen, with highest levels in spleen and lowest in heart. Expressed on the surface of T-cells.

Post-translational modifications. Sumoylated at Lys-20 by SUMO1 and at Lys-512 by SUMO1, SUMO2 and SUMO3. Sumoylation probably occurs sequentially, with that of Lys-20 preceding that of Lys-512. It does not alter association with heterochromatin, but is required for the repression of transcription.

Domain organisation. The BEN domain 4 is necessary and sufficient for the localization of BEND3 to heterochromatic regions.

RefSeq proteins (2): NP_001073919, NP_001354243* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018379	BEN_domain	Domain
IPR033583	BEND3	Family

Pfam: PF10523

UniProt features (54 total): cross-link 18, helix 16, mutagenesis site 5, domain 4, modified residue 3, sequence conflict 2, region of interest 2, chain 1, strand 1, turn 1, short sequence motif 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7W27	X-RAY DIFFRACTION	1.49
5JNO	X-RAY DIFFRACTION	2.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T5X7-F1	65.11	0.21

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 (21): 489, 20, 20, 20, 41, 56, 58, 73, 128, 129, 137, 142, 158, 176, 427, 512, 512, 528, 700, 164 …

Mutagenesis-validated functional residues (5):

Position	Phenotype
20	partial loss of sumoylation. almost complete loss of sumoylation, partial loss of transcription repression, no effect on
56	loss of nuclear localization.
57	loss of nuclear localization.
58	loss of nuclear localization.
512	partial loss of sumoylation. almost complete loss of sumoylation, partial loss of transcription repression, no effect on

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 141 (showing top): GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, GOBP_DNA_METHYLATION_DEPENDENT_CONSTITUTIVE_HETEROCHROMATIN_FORMATION, GOBP_POSITIVE_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS, GOBP_NUCLEUS_ORGANIZATION, GOBP_NUCLEOSIDE_TRIPHOSPHATE_METABOLIC_PROCESS, GOBP_PROTEIN_HOMOOLIGOMERIZATION, RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP, GOBP_REGULATION_OF_NUCLEOTIDE_METABOLIC_PROCESS, GOBP_CHROMATIN_REMODELING, GOBP_PURINE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_HETEROCHROMATIN_ORGANIZATION, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION

GO Biological Process (6): negative regulation of transcription by RNA polymerase II (GO:0000122), rDNA heterochromatin formation (GO:0000183), DNA methylation-dependent constitutive heterochromatin formation (GO:0006346), protein homooligomerization (GO:0051260), positive regulation of ATP metabolic process (GO:1903580), chromatin organization (GO:0006325)

GO Molecular Function (3): rDNA binding (GO:0000182), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (4): heterochromatin (GO:0000792), nucleoplasm (GO:0005654), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
facultative heterochromatin formation	1
nucleolar chromatin organization	1
constitutive heterochromatin formation	1
protein complex oligomerization	1
ATP metabolic process	1
positive regulation of purine nucleotide metabolic process	1
regulation of ATP metabolic process	1
cellular component organization	1
sequence-specific double-stranded DNA binding	1
nucleic acid binding	1
binding	1
chromatin	1
cellular anatomical structure	1
intracellular membraneless organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

616 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BEND3	CLDN5	O00501	577
BEND3	NACC2	Q96BF6	463
BEND3	TJP1	Q07157	447
BEND3	OCLN	Q16625	444
BEND3	RTN4IP1	Q8WWV3	425
BEND3	ZBTB10	Q96DT7	423
BEND3	BEND5	Q7L4P6	421
BEND3	BANP	Q8N9N5	415
BEND3	APCDD1	Q8J025	407
BEND3	DEFB1	P60022	403
BEND3	SCML4	Q8N228	395
BEND3	MLEC	Q14165	394
BEND3	MORC3	Q14149	387
BEND3	NACC1	Q96RE7	374
BEND3	ZBTB4	Q9P1Z0	372

IntAct

80 interactions, top by confidence:

A	B	Type	Score
MORN4	BEND3	psi-mi:“MI:0915”(physical association)	0.720
BEND3	MORN4	psi-mi:“MI:0915”(physical association)	0.720
HOXC9	AHCYL1	psi-mi:“MI:0914”(association)	0.640
FAM161A	BEND3	psi-mi:“MI:0915”(physical association)	0.560
BEND3	FAM161A	psi-mi:“MI:0915”(physical association)	0.560
BEND3	MCRS1	psi-mi:“MI:0915”(physical association)	0.560
BEND3	DPY30	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	BEND3	psi-mi:“MI:0915”(physical association)	0.560
FOXP3	FOXP2	psi-mi:“MI:0914”(association)	0.530
TRPS1	MTA2	psi-mi:“MI:0914”(association)	0.530
BEND3	PDIA6	psi-mi:“MI:0915”(physical association)	0.400
BEND3	BEND3	psi-mi:“MI:0915”(physical association)	0.370
Cenpf	RANBP2	psi-mi:“MI:0914”(association)	0.350
Septin11	SEPTIN10	psi-mi:“MI:0914”(association)	0.350
CFAP97	CSNK2A1	psi-mi:“MI:0914”(association)	0.350
NFATC1	SMARCA5	psi-mi:“MI:0914”(association)	0.350
NS1	ESYT2	psi-mi:“MI:0914”(association)	0.350
MKI67	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
ZNF785	CASK	psi-mi:“MI:0914”(association)	0.350
MAP7D2	ECI2	psi-mi:“MI:0914”(association)	0.350
USP21	ANKRD28	psi-mi:“MI:0914”(association)	0.350
IMMP2L	ANKHD1-EIF4EBP3	psi-mi:“MI:0914”(association)	0.350
rep	VWA8	psi-mi:“MI:0914”(association)	0.350
GRHL1	POLRMT	psi-mi:“MI:0914”(association)	0.350
CEP135	MCRIP1	psi-mi:“MI:0914”(association)	0.350

BioGRID (144): BEND3 (Two-hybrid), FAM161A (Two-hybrid), MORN4 (Two-hybrid), BEND3 (Affinity Capture-MS), BEND3 (Affinity Capture-MS), BEND3 (Affinity Capture-MS), BEND3 (Affinity Capture-MS), BEND3 (Affinity Capture-MS), BAZ2A (Affinity Capture-Western), BEND3 (Affinity Capture-Western), SMARCA5 (Affinity Capture-Western), BEND3 (Affinity Capture-Western), USP21 (Affinity Capture-Western), BEND3 (Affinity Capture-MS), BEND3 (Affinity Capture-MS)

ESM2 similar proteins: A0JN76, A2A5N8, A4IFA3, A4IGY9, D2EAC2, D3ZWK4, E1C2V1, O15060, O60290, O70445, O75132, P86452, Q08C99, Q0IJ29, Q13075, Q3UPF5, Q5BIW4, Q5T5X7, Q5T7W0, Q5TKR9, Q6DJS0, Q6EKJ0, Q6NRM8, Q6PAL0, Q6YI93, Q7Z2W4, Q7ZWZ4, Q801P1, Q80WQ9, Q80YY7, Q86UP8, Q8BZ21, Q8C4P0, Q8CFL8, Q8N8K9, Q8NCP5, Q8WML3, Q92794, Q96MP5, Q96Q42

Diamond homologs: Q5T5X7, Q6PAL0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 98 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
SUMOylation of chromatin organization proteins	5	12.4×	5e-03
SUMOylation of DNA damage response and repair proteins	5	11.4×	5e-03
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)	5	11.4×	5e-03
DNA Repair	6	9.2×	5e-03

GO biological processes:

GO term	Partners	Fold	FDR
chromatin remodeling	9	7.6×	6e-04
transcription by RNA polymerase II	8	6.6×	4e-03
DNA damage response	9	5.6×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	106
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1047881	GRCh37/hg19 6q21(chr6:107331934-108121759)	Pathogenic

SpliceAI

864 predictions. Top by Δscore:

Variant	Effect	Δscore
6:107098545:CCTCA:C	donor_loss	1.0000
6:107098546:CTCAC:C	donor_loss	1.0000
6:107098547:TCA:T	donor_loss	1.0000
6:107098548:CACC:C	donor_loss	1.0000
6:107098549:A:AC	donor_gain	1.0000
6:107098550:C:CC	donor_gain	1.0000
6:107098550:C:CT	donor_loss	1.0000
6:107098550:CCT:C	donor_gain	1.0000
6:107098568:T:TA	donor_gain	1.0000
6:107098749:TAGAA:T	acceptor_gain	1.0000
6:107098750:AGAA:A	acceptor_gain	1.0000
6:107098751:GAA:G	acceptor_gain	1.0000
6:107098752:AA:A	acceptor_gain	1.0000
6:107098752:AAC:A	acceptor_loss	1.0000
6:107098753:ACT:A	acceptor_loss	1.0000
6:107098754:C:CC	acceptor_gain	1.0000
6:107098756:G:C	acceptor_gain	1.0000
6:107098756:G:GC	acceptor_gain	1.0000
6:107098760:C:CT	acceptor_gain	1.0000
6:107099243:TTTTA:T	donor_loss	1.0000
6:107099244:TTTAC:T	donor_loss	1.0000
6:107099245:TTAC:T	donor_loss	1.0000
6:107099246:TACC:T	donor_loss	1.0000
6:107099247:A:C	donor_loss	1.0000
6:107099248:CCTT:C	donor_gain	1.0000
6:107099292:TTCCG:T	acceptor_gain	1.0000
6:107099294:CCG:C	acceptor_gain	1.0000
6:107099295:CG:C	acceptor_gain	1.0000
6:107099295:CGC:C	acceptor_gain	1.0000
6:107099297:C:CC	acceptor_gain	1.0000

AlphaMissense

5470 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:107068749:C:A	R814S	1.000
6:107068749:C:G	R814S	1.000
6:107068750:C:A	R814M	1.000
6:107068750:C:G	R814T	1.000
6:107068760:G:T	R811S	1.000
6:107068762:C:G	R810P	1.000
6:107068763:G:T	R810S	1.000
6:107068764:G:C	C809W	1.000
6:107068765:C:T	C809Y	1.000
6:107068766:A:G	C809R	1.000
6:107068767:C:A	R808S	1.000
6:107068767:C:G	R808S	1.000
6:107068768:C:A	R808M	1.000
6:107068770:C:A	E807D	1.000
6:107068770:C:G	E807D	1.000
6:107068771:T:A	E807V	1.000
6:107068771:T:G	E807A	1.000
6:107068772:C:T	E807K	1.000
6:107068774:T:A	D806V	1.000
6:107068774:T:C	D806G	1.000
6:107068774:T:G	D806A	1.000
6:107068775:C:A	D806Y	1.000
6:107068775:C:G	D806H	1.000
6:107068777:A:C	I805S	1.000
6:107068777:A:T	I805N	1.000
6:107068779:G:C	S804R	1.000
6:107068779:G:T	S804R	1.000
6:107068781:T:G	S804R	1.000
6:107068788:A:C	C801W	1.000
6:107068790:A:G	C801R	1.000

dbSNP variants (sampled 300 via entrez): RS1000026691 (6:107094391 G>A,C,T), RS1000243690 (6:107100839 G>T), RS1000364027 (6:107076863 C>T), RS1000487326 (6:107071199 C>T), RS1000551399 (6:107110896 G>A), RS1000604681 (6:107071460 C>A,T), RS1000704111 (6:107105632 A>T), RS1000917125 (6:107092958 C>T), RS1001029654 (6:107093223 G>A), RS1001047965 (6:107111069 G>T), RS1001240972 (6:107087098 G>A), RS1001243143 (6:107082125 T>G), RS1001298588 (6:107081799 A>G), RS1001446405 (6:107115903 G>C), RS1001485069 (6:107075848 T>G)

Disease associations

OMIM: gene MIM:616374 | disease phenotypes: MIM:209850

GenCC curated gene-disease

Mondo (1): autism (MONDO:0005260)

Orphanet (0):

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000717	Autism

GWAS associations

15 associations (top):

Study	Trait	p-value
GCST003014_7	Postprandial triglyceride response to high fat diet meal	4.000000e-07
GCST004609_75	Monocyte percentage of white cells	1.000000e-11
GCST006702_7	Parental longevity (combined parental age at death)	4.000000e-08
GCST009379_56	Type 2 diabetes	8.000000e-09
GCST010244_428	Triglyceride levels	1.000000e-09
GCST010702_55	Subcortical volume (MOSTest)	4.000000e-12
GCST010703_326	Brain morphology (MOSTest)	1.000000e-10
GCST90002388_99	Lymphocyte count	5.000000e-26
GCST90002389_329	Lymphocyte percentage of white cells	3.000000e-25
GCST90002396_331	Mean reticulocyte volume	3.000000e-28
GCST90002397_471	Mean spheric corpuscular volume	1.000000e-14
GCST90002399_300	Neutrophil percentage of white cells	1.000000e-15
GCST90002405_200	Reticulocyte count	5.000000e-12
GCST90002406_219	Reticulocyte fraction of red cells	3.000000e-10
GCST90020026_136	Hip index	6.000000e-09

EFO canonical traits (12, from GWAS)

EFO ID	Trait name
EFO:0007681	triglyceride change measurement
EFO:0007684	response to high fat food intake
EFO:0007989	monocyte percentage of leukocytes
EFO:0007796	parental longevity
EFO:0004530	triglyceride measurement
EFO:0004346	neuroimaging measurement
EFO:0004587	lymphocyte count
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0010701	mean reticulocyte volume
EFO:0007990	neutrophil percentage of leukocytes
EFO:0007986	reticulocyte count
EFO:0008039	BMI-adjusted hip circumference

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724790 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases methylation, affects expression	5
(+)-JQ1 compound	decreases expression	3
Estradiol	increases expression	3
bisphenol A	increases expression, increases methylation	2
entinostat	increases expression, affects cotreatment	2
aristolochic acid I	decreases expression	1
afuresertib	decreases expression	1
FR900359	increases phosphorylation	1
TAK-243	decreases sumoylation	1
dicrotophos	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Vorinostat	decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases expression	1
Caffeine	increases phosphorylation	1
Carbamazepine	affects expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1

ChEMBL screening assays

6 unique, capped per target: 6 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5697533	Binding	Inhibition of BEND3 (unknown origin) assessed as fold change at 10 uM incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. — Nature

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SF12	HAP1 BEND3 (-) 1	Cancer cell line	Male
CVCL_SF13	HAP1 BEND3 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00211796	PHASE4	COMPLETED	Divalproex Sodium ER in Adult Autism
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747	PHASE4	COMPLETED	Minocycline to Treat Childhood Regressive Autism
NCT00576732	PHASE4	COMPLETED	A Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753	PHASE4	COMPLETED	Atomoxetine, Placebo and Parent Management Training in Autism
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383	PHASE4	UNKNOWN	Treatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977	PHASE4	UNKNOWN	Study to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925	PHASE4	UNKNOWN	An Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565	PHASE4	COMPLETED	Dose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT00036231	PHASE3	TERMINATED	Synthetic Human Secretin in Children With Autism and Gastrointestinal Dysfunction
NCT00036244	PHASE3	COMPLETED	Synthetic Human Secretin in Children With Autism
NCT00065884	PHASE3	UNKNOWN	Valproate Response in Aggressive Autistic Adolescents
NCT00065962	PHASE3	COMPLETED	Secretin for the Treatment of Autism
NCT00252603	PHASE3	COMPLETED	Galantamine Versus Placebo in Childhood Autism
NCT00346736	PHASE3	COMPLETED	Use of Acupuncture In Children With Autistic Spectrum Disorder
NCT00352248	PHASE3	COMPLETED	Randomized Controlled Trial of Acupuncture Versus Sham Acupuncture in Autistic Spectrum Disorder
NCT00352352	PHASE3	COMPLETED	Use of Acupuncture In Children With Autistic Spectrum Disorder
NCT00355329	PHASE3	COMPLETED	Randomized Control Trial of Using Tongue Acupuncture in Autistic Spectrum Disorder Using PET Scan for Clinical Correlation
NCT00498173	PHASE3	COMPLETED	Effectiveness of Atomoxetine in Treating ADHD Symptoms in Children and Adolescents With Autism
NCT00541346	PHASE3	COMPLETED	A Pilot Study of Daytrana TM in Children With Autism Co-Morbid for Attention Deficit Hyperactivity Disorder (ADHD) Symptoms