BEND7

Summary

BEND7 (BEN domain containing 7, HGNC:23514) is a protein-coding gene on chromosome 10p13, encoding BEN domain-containing protein 7 (Q8N7W2).

Predicted to enable DNA binding activity. Located in extracellular exosome.

Source: NCBI Gene 222389 — RefSeq curated summary.

At a glance

• GWAS associations: 14
• Clinical variants (ClinVar): 80 total — 1 likely-pathogenic
• MANE Select transcript: NM_001369863

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23514
Approved symbol	BEND7
Name	BEN domain containing 7
Location	10p13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40283
Ensembl gene	ENSG00000165626
Ensembl biotype	protein_coding
Entrez	222389

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 18 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000341083, ENST00000378605, ENST00000440282, ENST00000463303, ENST00000466271, ENST00000469555, ENST00000480703, ENST00000486542, ENST00000649551, ENST00000683141, ENST00000688845, ENST00000689161, ENST00000689491, ENST00000857065, ENST00000857066, ENST00000960588, ENST00000960589, ENST00000960590, ENST00000960591, ENST00000960592, ENST00000960593, ENST00000960594

RefSeq mRNA: 8 — MANE Select: NM_001369863 NM_001100912, NM_001369863, NM_001370075, NM_001378149, NM_001378150, NM_001378151, NM_001387359, NM_152751

CCDS: CCDS41490, CCDS7099, CCDS91214

Canonical transcript exons

ENST00000466271 — 9 exons

Exon	Start	End
ENSE00001094804	13480899	13481124
ENSE00001094808	13492611	13492876
ENSE00001094812	13496766	13496888
ENSE00001832630	13528473	13529014
ENSE00003541650	13447266	13447316
ENSE00003560713	13499778	13500080
ENSE00003580764	13452539	13452658
ENSE00003595805	13526138	13526221
ENSE00003932417	13441088	13441750

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 95.82.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9570 / max 29.7496, expressed in 888 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
108307	1.4653	756
108306	0.4918	295

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	95.82	gold quality
pancreatic ductal cell	CL:0002079	94.85	gold quality
jejunal mucosa	UBERON:0000399	93.34	gold quality
ileal mucosa	UBERON:0000331	92.00	gold quality
islet of Langerhans	UBERON:0000006	90.91	gold quality
parotid gland	UBERON:0001831	90.04	gold quality
left testis	UBERON:0004533	89.74	gold quality
right testis	UBERON:0004534	89.66	gold quality
gastrocnemius	UBERON:0001388	89.29	gold quality
epithelial cell of pancreas	CL:0000083	89.25	gold quality
adult mammalian kidney	UBERON:0000082	89.18	gold quality
ventricular zone	UBERON:0003053	89.17	gold quality
thyroid gland	UBERON:0002046	88.95	gold quality
caput epididymis	UBERON:0004358	88.78	gold quality
muscle of leg	UBERON:0001383	88.76	gold quality
left lobe of thyroid gland	UBERON:0001120	88.71	gold quality
kidney	UBERON:0002113	88.66	gold quality
testis	UBERON:0000473	88.53	gold quality
duodenum	UBERON:0002114	88.29	gold quality
right lobe of thyroid gland	UBERON:0001119	88.17	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.09	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.57	gold quality
pancreas	UBERON:0001264	87.39	gold quality
right lung	UBERON:0002167	86.56	gold quality
cortex of kidney	UBERON:0001225	86.55	gold quality
ganglionic eminence	UBERON:0004023	86.55	gold quality
metanephros cortex	UBERON:0010533	86.54	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.51	gold quality
minor salivary gland	UBERON:0001830	86.42	gold quality
saliva-secreting gland	UBERON:0001044	86.39	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.29
E-GEOD-137537	no	721.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting BEND7, 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-8485	100.00	77.57	4731
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-3913-3P	99.74	66.53	938
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-199A-5P	99.51	69.71	1107
HSA-MIR-199B-5P	99.51	69.74	1098
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-3196	98.96	63.91	326
HSA-MIR-219A-1-3P	98.91	67.87	639
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-655-5P	98.74	65.93	888
HSA-MIR-603	98.58	68.28	1603
HSA-MIR-197-3P	98.09	69.23	1004
HSA-MIR-6783-5P	97.67	67.21	1528
HSA-MIR-3620-5P	97.42	63.95	792
HSA-MIR-6824-5P	97.41	68.43	583

Literature-anchored findings (GeneRIF, showing 1)

• These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 x 10(-14), rs1426654) and SLC45A2 (minimum p = 9.71 x 10(-10), rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 x 10(-9), rs6602666). (PMID:28300201)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	bend7	ENSDARG00000063186
mus_musculus	Bend7	ENSMUSG00000048186

Protein

Protein identifiers

BEN domain-containing protein 7 — Q8N7W2 (reviewed: Q8N7W2)

All UniProt accessions (10): A0A0A0MSS7, A0A3B3IU36, A0A804HI39, A0A804HIL1, A0A804HIW4, A0A804HKD1, Q8N7W2, A0A8I5KQX9, A0A8I5KUV1, A0AAK2PQJ4

UniProt curated annotations — full annotation on UniProt →

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N7W2-4	1	yes
Q8N7W2-2	2
Q8N7W2-3	3

RefSeq proteins (8): NP_001094382, NP_001356792, NP_001357004, NP_001365078, NP_001365079, NP_001365080, NP_001374288, NP_689964 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018379	BEN_domain	Domain
IPR053072	BEN_domain_protein_7	Family

Pfam: PF10523

UniProt features (21 total): compositionally biased region 5, cross-link 4, splice variant 4, modified residue 2, sequence variant 2, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7W2-F1	62.17	0.25

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): 328, 16, 56, 85, 243, 324

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): chr10p13, NRF2_Q4, TGGAAA_NFAT_Q4_01, YOSHIMURA_MAPK8_TARGETS_UP, ZHAN_MULTIPLE_MYELOMA_MS_UP, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, MAFG_TARGET_GENES, MIR8485, MIR559, MIR9983_3P, MIR548Y, MIR548BB_5P, MIR548AR_5P, MIR548AD_5P_MIR548AE_5P_MIR548AY_5P_MIR548B_5P_MIR548D_5P

GO Biological Process (0):

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

GO Cellular Component (1): extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
binding	1
extracellular vesicle	1

Protein interactions and networks

STRING

432 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BEND7	BEND6	Q5SZJ8	649
BEND7	TATDN3	Q17R31	625
BEND7	SMIM12	Q96EX1	616
BEND7	LYPD6B	Q8NI32	615
BEND7	OTOL1	A6NHN0	564
BEND7	ANGEL2	Q5VTE6	558
BEND7	SHISA4	Q96DD7	530
BEND7	MNMIP1	A4FU49	524
BEND7	RPS6KC1	Q96S38	510
BEND7	ST8SIA5	O15466	508
BEND7	KATNAL2	Q8IYT4	490
BEND7	SHLD1	Q8IYI0	478
BEND7	PRPF18	Q99633	474
BEND7	PHYH	O14832	459
BEND7	CLEC2L	P0C7M8	458

IntAct

41 interactions, top by confidence:

A	B	Type	Score
RBBP4	CDK2AP1	psi-mi:“MI:0914”(association)	0.790
ZNF219	CDK2AP1	psi-mi:“MI:0914”(association)	0.640
BEND7	NIF3L1	psi-mi:“MI:0915”(physical association)	0.620
NIF3L1	BEND7	psi-mi:“MI:0915”(physical association)	0.620
BEND7	LYAR	psi-mi:“MI:0915”(physical association)	0.550
BEND7	EIF1AD	psi-mi:“MI:0915”(physical association)	0.550
MBD3L1	CDK2AP1	psi-mi:“MI:0914”(association)	0.530
BEND7	LRP4	psi-mi:“MI:0914”(association)	0.530
BEND7	PLEKHF2	psi-mi:“MI:0915”(physical association)	0.490
BEND7	PSMF1	psi-mi:“MI:0915”(physical association)	0.490
NAA30	BEND7	psi-mi:“MI:0915”(physical association)	0.400
BEND7		psi-mi:“MI:0915”(physical association)	0.370
BEND7	E7	psi-mi:“MI:0915”(physical association)	0.370
BEND7	MBD2	psi-mi:“MI:0915”(physical association)	0.370
BEND7	rep	psi-mi:“MI:0915”(physical association)	0.370
SDCBP2	BEND7	psi-mi:“MI:0915”(physical association)	0.370
EMD	BEND7	psi-mi:“MI:0915”(physical association)	0.370
U2AF2	BEND7	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (138): BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid), BEND7 (Two-hybrid)

ESM2 similar proteins: A0A5K7RLP0, A1YEX3, A7YWH3, B1WBU4, O15151, O35618, O43298, O88850, P24278, P97303, Q01954, Q0V8G8, Q15916, Q17RG1, Q562E2, Q5RC05, Q5RDQ6, Q5SXH7, Q5TC79, Q5VYS8, Q5W0Q7, Q5XIN1, Q6ZPY5, Q6ZSB9, Q6ZU67, Q7ZUW7, Q7ZYI3, Q8BLK9, Q8BSV3, Q8IW35, Q8K088, Q8N680, Q8N7W2, Q8TCN5, Q8VHI4, Q8WW38, Q90W33, Q96BR9, Q96S38, Q99ME3

Diamond homologs: O35260, Q562B4, Q7TSZ8, Q8BSV3, Q8N7W2, Q96BF6, Q96RE7, Q9DCM7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	64
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
144993	GRCh38/hg38 10p13(chr10:12333253-13948472)x1	Likely pathogenic

SpliceAI

2084 predictions. Top by Δscore:

Variant	Effect	Δscore
10:13447324:T:C	acceptor_gain	1.0000
10:13447324:T:TC	acceptor_gain	1.0000
10:13452659:C:CC	acceptor_gain	1.0000
10:13481121:CTGG:C	acceptor_gain	1.0000
10:13481125:C:CC	acceptor_gain	1.0000
10:13492609:A:AC	donor_gain	1.0000
10:13492609:ACAT:A	donor_gain	1.0000
10:13492610:C:CC	donor_gain	1.0000
10:13492610:CAT:C	donor_gain	1.0000
10:13492610:CATC:C	donor_gain	1.0000
10:13447261:TTTA:T	donor_loss	0.9900
10:13447262:TTA:T	donor_loss	0.9900
10:13447263:TA:T	donor_loss	0.9900
10:13447264:A:AT	donor_loss	0.9900
10:13447317:CTG:C	acceptor_gain	0.9900
10:13447320:C:CC	acceptor_gain	0.9900
10:13447327:C:CT	acceptor_gain	0.9900
10:13447331:C:CT	acceptor_gain	0.9900
10:13452549:TTTTA:T	donor_gain	0.9900
10:13480935:T:A	donor_gain	0.9900
10:13481129:C:CT	acceptor_gain	0.9900
10:13481130:A:T	acceptor_gain	0.9900
10:13492603:CAACT:C	donor_loss	0.9900
10:13492604:AACTT:A	donor_loss	0.9900
10:13492605:ACTT:A	donor_loss	0.9900
10:13492606:CTTA:C	donor_loss	0.9900
10:13492607:T:TC	donor_loss	0.9900
10:13492608:TACAT:T	donor_loss	0.9900
10:13492609:A:T	donor_loss	0.9900
10:13492610:C:CG	donor_loss	0.9900

AlphaMissense

2683 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000038632 (10:13442157 C>A), RS1000052092 (10:13446836 G>T), RS1000121010 (10:13473303 C>T), RS1000133946 (10:13465900 TG>T), RS1000138149 (10:13460465 A>T), RS1000168607 (10:13473459 T>A), RS1000180078 (10:13515314 C>T), RS1000220897 (10:13473765 G>A), RS1000223578 (10:13513087 C>T), RS1000236742 (10:13509116 C>A,G,T), RS1000257889 (10:13478071 G>C), RS1000281178 (10:13489427 T>C,G), RS1000294653 (10:13515032 A>G), RS1000411041 (10:13463005 C>T), RS1000436789 (10:13484289 A>G)

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

14 associations (top):

Study	Trait	p-value
GCST002337_139	Amyotrophic lateral sclerosis (sporadic)	7.000000e-07
GCST004219_3	Skin pigmentation	5.000000e-09
GCST006630_21	Diastolic blood pressure	1.000000e-13
GCST006896_8	Free thyroxine concentration	8.000000e-07
GCST007327_53	Smoking status (ever vs never smokers)	1.000000e-08
GCST010320_67	PR interval	2.000000e-07
GCST010321_19	PR interval	4.000000e-08
GCST012310_17	Schizophrenia x sex interaction	6.000000e-06
GCST90002383_479	Hematocrit	8.000000e-11
GCST90002384_182	Hemoglobin	2.000000e-12
GCST90002389_362	Lymphocyte percentage of white cells	3.000000e-11
GCST90002398_168	Neutrophil count	2.000000e-18
GCST90002399_91	Neutrophil percentage of white cells	4.000000e-10
GCST90002407_87	White blood cell count	4.000000e-16

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0004318	smoking behavior
EFO:0004462	PR interval
EFO:0008343	sex interaction measurement
EFO:0004348	hematocrit
EFO:0004509	hemoglobin measurement
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0004833	neutrophil count
EFO:0007990	neutrophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases expression, increases methylation, affects cotreatment	4
trichostatin A	affects cotreatment, decreases expression, increases expression	3
sodium arsenite	decreases expression, increases expression	3
Nickel	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
deoxynivalenol	increases expression	1
terbufos	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	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
dorsomorphin	affects cotreatment, decreases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1
Parathion	increases methylation	1
Silicon Dioxide	decreases expression	1
Silver	increases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Tretinoin	increases expression	1
Cyclosporine	increases expression	1
Copper Sulfate	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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