BEND5

Summary

BEND5 (BEN domain containing 5, HGNC:25668) is a protein-coding gene on chromosome 1p33, encoding BEN domain-containing protein 5 (Q7L4P6). Acts as a transcriptional repressor.

Predicted to enable DNA binding activity. Involved in negative regulation of DNA-templated transcription. Predicted to be located in Golgi apparatus.

Source: NCBI Gene 79656 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total — 1 likely-pathogenic
• MANE Select transcript: NM_024603

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25668
Approved symbol	BEND5
Name	BEN domain containing 5
Location	1p33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11588
Ensembl gene	ENSG00000162373
Ensembl biotype	protein_coding
OMIM	621198
Entrez	79656

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding_CDS_not_defined, 2 protein_coding, 2 retained_intron

ENST00000371833, ENST00000463562, ENST00000476079, ENST00000476096, ENST00000480399, ENST00000489956, ENST00000936956

RefSeq mRNA: 5 — MANE Select: NM_024603 NM_001302082, NM_001349793, NM_001349794, NM_001349795, NM_024603

CCDS: CCDS552

Canonical transcript exons

ENST00000371833 — 6 exons

Exon	Start	End
ENSE00001754100	48758900	48759284
ENSE00001813541	48727519	48728043
ENSE00002205514	48776606	48776891
ENSE00003469862	48761337	48761470
ENSE00003558898	48742623	48742771
ENSE00003596253	48736239	48736452

Expression profiles

Bgee: expression breadth ubiquitous, 207 present calls, max score 92.72.

FANTOM5 (CAGE): breadth broad, TPM avg 2.7340 / max 71.7681, expressed in 682 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12259	1.2724	482
12257	1.1750	454
12260	0.2866	162

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	92.72	gold quality
right frontal lobe	UBERON:0002810	90.77	gold quality
cortical plate	UBERON:0005343	90.58	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.23	gold quality
anterior cingulate cortex	UBERON:0009835	90.17	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.14	gold quality
cingulate cortex	UBERON:0003027	90.12	gold quality
prefrontal cortex	UBERON:0000451	89.95	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.18	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.65	gold quality
neocortex	UBERON:0001950	88.63	gold quality
frontal cortex	UBERON:0001870	88.47	gold quality
adenohypophysis	UBERON:0002196	88.18	gold quality
cerebral cortex	UBERON:0000956	87.09	gold quality
middle temporal gyrus	UBERON:0002771	87.03	gold quality
ventricular zone	UBERON:0003053	87.00	gold quality
pituitary gland	UBERON:0000007	86.73	gold quality
left ovary	UBERON:0002119	86.64	gold quality
descending thoracic aorta	UBERON:0002345	86.43	gold quality
endothelial cell	CL:0000115	86.24	silver quality
muscle layer of sigmoid colon	UBERON:0035805	86.05	gold quality
Brodmann (1909) area 23	UBERON:0013554	85.91	gold quality
amygdala	UBERON:0001876	85.54	gold quality
right ovary	UBERON:0002118	85.10	gold quality
telencephalon	UBERON:0001893	84.98	gold quality
forebrain	UBERON:0001890	84.67	gold quality
primary visual cortex	UBERON:0002436	84.51	gold quality
embryo	UBERON:0000922	84.33	gold quality
thoracic aorta	UBERON:0001515	83.96	gold quality
ascending aorta	UBERON:0001496	83.95	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.21
E-MTAB-6386	no	478.72
E-ENAD-17	no	209.35

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting BEND5, 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-4795-3P	100.00	74.62	4024
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-4742-5P	98.89	68.41	1542
HSA-MIR-6715B-3P	98.80	68.07	1204
HSA-MIR-4773	98.35	67.30	1710
HSA-MIR-4457	98.09	67.12	1274

Literature-anchored findings (GeneRIF, showing 1)

• Interaction between BEND5 and RBPJ suppresses breast cancer growth and metastasis via inhibiting Notch signaling. (PMID:35844785)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	bend5	ENSDARG00000075624
mus_musculus	Bend5	ENSMUSG00000028545
rattus_norvegicus	Bend5	ENSRNOG00000008025

Protein

Protein identifiers

BEN domain-containing protein 5 — Q7L4P6 (reviewed: Q7L4P6)

All UniProt accessions (2): A0A0S2Z5N0, Q7L4P6

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a transcriptional repressor.

Domain organisation. The BEN domain mediates DNA-binding.

Isoforms (2)

UniProt ID	Names	Canonical?
Q7L4P6-1	1	yes
Q7L4P6-2	2

RefSeq proteins (5): NP_001289011, NP_001336722, NP_001336723, NP_001336724, NP_078879* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018379	BEN_domain	Domain
IPR040391	BEND5	Family

Pfam: PF10523

UniProt features (7 total): chain 1, domain 1, coiled-coil region 1, modified residue 1, cross-link 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7L4P6-F1	74.20	0.40

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): 133, 258

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, SABATES_COLORECTAL_ADENOMA_DN, VECCHI_GASTRIC_CANCER_EARLY_DN, MODULE_48, MODULE_95, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, MODULE_69, ZHAN_MULTIPLE_MYELOMA_CD2_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, LIU_PROSTATE_CANCER_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, MODULE_37, MODULE_163

GO Biological Process (1): negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (2): DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (1): Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
nucleic acid binding	1
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

378 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BEND5	BEND6	Q5SZJ8	685
BEND5	TRIML1	Q8N9V2	582
BEND5	ATP10D	Q9P241	507
BEND5	BEND2	Q8NDZ0	507
BEND5	BANP	Q8N9N5	483
BEND5	DPEP2	Q9H4A9	479
BEND5	BEND3	Q5T5X7	421
BEND5	SHROOM3	Q8TF72	397
BEND5	ZNF625	Q96I27	397
BEND5	AGBL4	Q5VU57	390
BEND5	BEND4	Q6ZU67	370
BEND5	KCNH4	Q9UQ05	337
BEND5	NACC2	Q96BF6	336
BEND5	CCDC138	Q96M89	331
BEND5	C1QL2	Q7Z5L3	328
BEND5	MRPS24	P82668	328

IntAct

75 interactions, top by confidence:

A	B	Type	Score
PRKAB2	BEND5	psi-mi:“MI:0915”(physical association)	0.670
GORASP2	BEND5	psi-mi:“MI:0915”(physical association)	0.670
BEND5	PRKAB2	psi-mi:“MI:0915”(physical association)	0.670
BEND5	GORASP2	psi-mi:“MI:0915”(physical association)	0.670
BEND5	EIF3D	psi-mi:“MI:0915”(physical association)	0.560
BEND5	BUD31	psi-mi:“MI:0915”(physical association)	0.560
BEND5	RTP5	psi-mi:“MI:0915”(physical association)	0.560
BEND5	FAM161A	psi-mi:“MI:0915”(physical association)	0.560
BEND5	LCE1B	psi-mi:“MI:0915”(physical association)	0.560
UBE2I	BEND5	psi-mi:“MI:0915”(physical association)	0.560
BEND5	ZGPAT	psi-mi:“MI:0915”(physical association)	0.560
ZNF417	BEND5	psi-mi:“MI:0915”(physical association)	0.560
BEND5	VPS25	psi-mi:“MI:0915”(physical association)	0.560
BEND5	USP20	psi-mi:“MI:0915”(physical association)	0.560
RTP5	BEND5	psi-mi:“MI:0915”(physical association)	0.560
BEND5	UBE2I	psi-mi:“MI:0915”(physical association)	0.560
ZGPAT	BEND5	psi-mi:“MI:0915”(physical association)	0.560
BEND5	ZNF417	psi-mi:“MI:0915”(physical association)	0.560
EIF3D	BEND5	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (35): BEND5 (Two-hybrid), BEND5 (Two-hybrid), BEND5 (Two-hybrid), BEND5 (Two-hybrid), BEND5 (Two-hybrid), BEND5 (Two-hybrid), FAM161A (Two-hybrid), VPS25 (Two-hybrid), ZGPAT (Two-hybrid), ZNF417 (Two-hybrid), RTP5 (Two-hybrid), LCE1B (Two-hybrid), BEND5 (Two-hybrid), BEND5 (Two-hybrid), BEND5 (Two-hybrid)

ESM2 similar proteins: A1L131, A4IFK7, C5IJB0, D3ZND0, F1MX48, O60232, O95400, P35689, Q0VCT3, Q17QX2, Q2KIJ6, Q2YD98, Q3ZBK7, Q3ZBN4, Q4R4I0, Q53GS7, Q5EAN7, Q5FVK6, Q5PPF5, Q5RAS2, Q5T0F9, Q68F60, Q69ZT1, Q6AYI4, Q6NU18, Q6TLH3, Q7L4P6, Q7TMX5, Q8BL74, Q8BRN9, Q8BSI6, Q8C0R7, Q8C6D4, Q8N5A5, Q8R322, Q8VDM1, Q91VL8, Q91WA6, Q91WR3, Q969X0

Diamond homologs: Q3B8D4, Q7L4P6, Q8C6D4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1526949	GRCh37/hg19 1p34.1-32.3(chr1:45303358-52157856)	Likely pathogenic

SpliceAI

1475 predictions. Top by Δscore:

Variant	Effect	Δscore
1:48727908:T:TA	donor_gain	1.0000
1:48727909:C:A	donor_gain	1.0000
1:48728040:CACT:C	acceptor_gain	1.0000
1:48728042:CT:C	acceptor_gain	1.0000
1:48728044:C:CC	acceptor_gain	1.0000
1:48758892:GCAC:G	donor_loss	1.0000
1:48758893:CACT:C	donor_loss	1.0000
1:48758894:ACTC:A	donor_loss	1.0000
1:48758895:CT:C	donor_loss	1.0000
1:48758896:TCA:T	donor_loss	1.0000
1:48758897:CA:C	donor_loss	1.0000
1:48758898:A:AC	donor_gain	1.0000
1:48758898:A:AT	donor_loss	1.0000
1:48758899:C:CA	donor_loss	1.0000
1:48758899:C:CC	donor_gain	1.0000
1:48758899:C:CG	donor_loss	1.0000
1:48758899:CCG:C	donor_gain	1.0000
1:48758926:T:TA	donor_gain	1.0000
1:48761468:CTT:C	acceptor_gain	1.0000
1:48761469:TT:T	acceptor_gain	1.0000
1:48761469:TTC:T	acceptor_loss	1.0000
1:48761470:TC:T	acceptor_loss	1.0000
1:48761471:C:CC	acceptor_gain	1.0000
1:48761471:C:G	acceptor_loss	1.0000
1:48761471:C:T	acceptor_loss	1.0000
1:48761476:A:AC	acceptor_gain	1.0000
1:48761476:A:C	acceptor_gain	1.0000
1:48761479:C:CT	acceptor_gain	1.0000
1:48761480:A:AC	acceptor_gain	1.0000
1:48761480:A:C	acceptor_gain	1.0000

AlphaMissense

2762 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:48727934:T:A	K406N	1.000
1:48727934:T:G	K406N	1.000
1:48727935:T:A	K406I	1.000
1:48727936:T:C	K406E	1.000
1:48727936:T:G	K406Q	1.000
1:48727939:T:C	N405D	1.000
1:48727941:A:C	I404S	1.000
1:48727941:A:T	I404N	1.000
1:48727943:A:C	D403E	1.000
1:48727943:A:T	D403E	1.000
1:48727944:T:A	D403V	1.000
1:48727944:T:C	D403G	1.000
1:48727944:T:G	D403A	1.000
1:48727945:C:A	D403Y	1.000
1:48727945:C:G	D403H	1.000
1:48727945:C:T	D403N	1.000
1:48727946:C:A	M402I	1.000
1:48727946:C:G	M402I	1.000
1:48727946:C:T	M402I	1.000
1:48727947:A:C	M402R	1.000
1:48727947:A:G	M402T	1.000
1:48727947:A:T	M402K	1.000
1:48727950:A:C	I401S	1.000
1:48727950:A:G	I401T	1.000
1:48727950:A:T	I401N	1.000
1:48727951:T:A	I401F	1.000
1:48727952:T:A	K400N	1.000
1:48727952:T:G	K400N	1.000
1:48727953:T:A	K400I	1.000
1:48727954:T:C	K400E	1.000

dbSNP variants (sampled 300 via entrez): RS1000072865 (1:48737066 G>A), RS1000148165 (1:48734425 G>A), RS1000178764 (1:48752889 A>C), RS1000203442 (1:48769451 C>T), RS1000476389 (1:48776021 A>C), RS1000480839 (1:48754428 G>T), RS1000512862 (1:48754131 G>A,C), RS1000659883 (1:48755486 G>A), RS1000821120 (1:48749504 A>G), RS1000907045 (1:48728971 G>A), RS1001085484 (1:48774407 T>C), RS1001142167 (1:48760579 A>G), RS1001149120 (1:48751420 C>A,T), RS1001187351 (1:48776656 C>G,T), RS1001358916 (1:48730493 G>T)

Disease associations

OMIM: gene MIM:621198 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	4
trichostatin A	affects cotreatment, decreases expression	2
entinostat	decreases expression, affects cotreatment	2
Zoledronic Acid	decreases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Silicon Dioxide	decreases expression, increases expression	2
Cyclosporine	decreases expression, decreases methylation	2
chloroacetaldehyde	decreases expression	1
triphenyl phosphate	affects expression	1
terbufos	increases methylation	1
sodium arsenite	affects methylation	1
benzo(e)pyrene	increases methylation	1
adefovir dipivoxil	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
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Cidofovir	affects expression	1
Amphotericin B	decreases expression	1
Arsenicals	decreases expression	1
Atrazine	decreases expression	1
Cisplatin	affects expression	1
Clodronic Acid	increases expression	1
Fonofos	increases methylation	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	decreases expression	1
Oxygen	increases expression	1
Parathion	increases methylation	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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