ZBED5

Summary

ZBED5 (zinc finger BED-type containing 5, HGNC:30803) is a protein-coding gene on chromosome 11p15.4, encoding Zinc finger BED domain-containing protein 5 (Q49AG3).

This gene is unusual in that its coding sequence is mostly derived from Charlie-like DNA transposon; however, it does not appear to be an active DNA transposon as it is not flanked by terminal inverted repeats. The encoded protein is conserved among the mammalian Laurasiatheria branch. Multiple alternatively spliced variants, encoding the same protein, have been identified.

Source: NCBI Gene 58486 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_001143667

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30803
Approved symbol	ZBED5
Name	zinc finger BED-type containing 5
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Aliases	Buster1
Ensembl gene	ENSG00000236287
Ensembl biotype	protein_coding
OMIM	615251
Entrez	58486

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 15 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000413761, ENST00000432999, ENST00000525350, ENST00000526020, ENST00000526852, ENST00000528289, ENST00000530570, ENST00000533903, ENST00000533925, ENST00000534690, ENST00000876894, ENST00000876895, ENST00000876896, ENST00000876897, ENST00000931256, ENST00000931257, ENST00000931258, ENST00000931259, ENST00000931260

RefSeq mRNA: 2 — MANE Select: NM_001143667 NM_001143667, NM_021211

Canonical transcript exons

ENST00000413761 — 3 exons

Exon	Start	End
ENSE00001695798	10856144	10856257
ENSE00001803103	10852706	10855086
ENSE00002201728	10857862	10858053

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 97.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.6389 / max 468.4669, expressed in 1816 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
118665	32.9954	1811
118664	14.3471	1764
118663	0.2965	123

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibia	UBERON:0000979	97.28	gold quality
epithelium of nasopharynx	UBERON:0001951	97.19	gold quality
ganglionic eminence	UBERON:0004023	96.86	gold quality
tongue squamous epithelium	UBERON:0006919	96.83	gold quality
hair follicle	UBERON:0002073	96.58	gold quality
left ovary	UBERON:0002119	96.31	gold quality
upper leg skin	UBERON:0004262	96.27	gold quality
body of uterus	UBERON:0009853	96.21	gold quality
germinal epithelium of ovary	UBERON:0001304	96.03	gold quality
ventricular zone	UBERON:0003053	95.95	gold quality
right ovary	UBERON:0002118	95.92	gold quality
metanephros cortex	UBERON:0010533	95.89	gold quality
skin of hip	UBERON:0001554	95.70	gold quality
descending thoracic aorta	UBERON:0002345	95.68	gold quality
lymph node	UBERON:0000029	95.67	gold quality
left lobe of thyroid gland	UBERON:0001120	95.65	gold quality
right lobe of thyroid gland	UBERON:0001119	95.64	gold quality
visceral pleura	UBERON:0002401	95.49	gold quality
ovary	UBERON:0000992	95.47	gold quality
thyroid gland	UBERON:0002046	95.46	gold quality
mucosa of stomach	UBERON:0001199	95.34	gold quality
right uterine tube	UBERON:0001302	95.34	gold quality
cortical plate	UBERON:0005343	95.27	gold quality
endocervix	UBERON:0000458	95.15	gold quality
vermiform appendix	UBERON:0001154	95.15	gold quality
endometrium	UBERON:0001295	95.10	gold quality
calcaneal tendon	UBERON:0003701	95.09	gold quality
rectum	UBERON:0001052	95.06	gold quality
parietal pleura	UBERON:0002400	95.04	gold quality
embryo	UBERON:0000922	95.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.57
E-MTAB-6386	no	601.56

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2602.1	ZBED5	BED zinc finger factors

JASPAR matrix evidence (PMIDs): PMID:39605368

miRNA regulators (miRDB)

11 targeting ZBED5, 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-4799-5P	99.82	70.60	2663
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-487A-5P	98.85	69.37	993
HSA-MIR-487B-5P	98.85	69.48	987
HSA-MIR-605-5P	98.79	68.24	1161
HSA-MIR-548AO-5P	98.55	69.57	1362
HSA-MIR-548AX	98.55	69.58	1362
HSA-MIR-1248	98.47	67.54	1314
HSA-MIR-3614-3P	97.81	67.15	582
HSA-MIR-424-3P	97.20	65.86	385
HSA-MIR-600	97.07	66.73	1259

Cross-species orthologs

0 orthologs

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), ZMYM5 (ENSG00000132950), THAP12 (ENSG00000137492), ZMYM4 (ENSG00000146463), ZMYM3 (ENSG00000147130), ZMYM6 (ENSG00000163867), KIAA1958 (ENSG00000165185), GTF2IRD2B (ENSG00000174428), EPM2AIP1 (ENSG00000178567), GTF2IRD2 (ENSG00000196275), ZMYM1 (ENSG00000197056), QRICH1 (ENSG00000198218), FAM200C (ENSG00000221886), FAM200A (ENSG00000221909), SCAND3 (ENSG00000232040), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Protein

Protein identifiers

Zinc finger BED domain-containing protein 5 — Q49AG3 (reviewed: Q49AG3)

Alternative names: Transposon-derived Buster1 transposase-like protein

All UniProt accessions (5): Q49AG3, E9PJ57, E9PJT5, E9PM71, E9PNT1

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be derived from an ancient transposon that has lost its ability to translocate.

RefSeq proteins (2): NP_001137139, NP_067034 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003656	Znf_BED	Domain
IPR012337	RNaseH-like_sf	Homologous_superfamily

Pfam: PF02892

UniProt features (10 total): binding site 4, sequence variant 4, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q49AG3-F1	81.57	0.50

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (4): 132; 135; 152; 157

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 134 (showing top): MODULE_493, GGGTGGRR_PAX4_03, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, TAANNYSGCG_UNKNOWN, EVI1_04, MODULE_332, MARSON_BOUND_BY_FOXP3_STIMULATED, GCGSCMNTTT_UNKNOWN, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, KIM_WT1_TARGETS_DN, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN, HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN, WHITFIELD_CELL_CYCLE_S

GO Biological Process (0):

GO Molecular Function (3): DNA binding (GO:0003677), zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
transition metal ion binding	1
cation binding	1

Protein interactions and networks

STRING

474 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZBED5	ZBED10P	Q96FA7	571
ZBED5	TMPRSS11D	O60235	479
ZBED5	MAGEB17	A8MXT2	478
ZBED5	ZBED6	P86452	447
ZBED5	TTC23L	Q6PF05	447
ZBED5	ZSCAN30	Q86W11	431
ZBED5	ZNF850	A8MQ14	420
ZBED5	NUDT8	Q8WV74	419
ZBED5	ZNF235	Q14590	418
ZBED5	TMEM177	Q53S58	396
ZBED5	ZBED2	Q9BTP6	393
ZBED5	RNF175	Q8N4F7	393
ZBED5	ZNF770	Q6IQ21	393
ZBED5	C6orf136	Q5SQH8	391
ZBED5	ZBED4	O75132	373

IntAct

12 interactions, top by confidence:

A	B	Type	Score
ZBED5	AMIGO1	psi-mi:“MI:0915”(physical association)	0.400
ZBED5	SMAD4	psi-mi:“MI:0915”(physical association)	0.370
M		psi-mi:“MI:0914”(association)	0.350
FGFR3	U2SURP	psi-mi:“MI:0914”(association)	0.350
AFG2A	ESYT2	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350
ZBED5	sdhA	psi-mi:“MI:0915”(physical association)	0.000
ZBED5	tkt1	psi-mi:“MI:0915”(physical association)	0.000
	ZBED5	psi-mi:“MI:0915”(physical association)	0.000
ZBED5		psi-mi:“MI:0915”(physical association)	0.000
ERG	ZBED5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): ZBED5 (Affinity Capture-MS), ZBED5 (Affinity Capture-MS), ZBED5 (Proximity Label-MS), AMIGO1 (Affinity Capture-MS), ZBED5 (Two-hybrid), ZBED5 (Affinity Capture-MS), ZBED5 (Affinity Capture-MS), ZBED5 (Affinity Capture-MS), ZBED5 (Affinity Capture-RNA), ZBED5 (Two-hybrid)

ESM2 similar proteins: A3KMX0, A4IFA3, A4IGY9, A4Z943, A4Z944, B8QB46, D2EAC2, E1C2V1, O43422, O60290, P10911, P35125, P86452, Q13075, Q2NKX8, Q3UPF5, Q49AG3, Q5FWF4, Q5SVZ6, Q5T890, Q5TKR9, Q6DJS0, Q6EKJ0, Q6R2W3, Q6YI93, Q7Z2W4, Q80WE4, Q86UP8, Q86VD1, Q8BZ21, Q8N8K9, Q8QMP8, Q8TDB6, Q8WML3, Q92794, Q96JM7, Q96JS3, Q99388, Q99NI3, Q9CUX1

Diamond homologs: A4Z943, A4Z944, A4Z945, O95789, P0CF97, Q49AG3, Q4R6P1, Q6R2W3, Q8IZ13, Q8TCP9, A2A791, A6QPH9, Q14202, Q3U2E2, Q4R3D6, Q5RDJ2, Q5SVZ6, Q5VZL5, Q9CU65, Q9JLM4, Q9UBW7, Q9UJ78, P17029, Q4KLI1, Q5R670, Q8BGS3, A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

981 predictions. Top by Δscore:

Variant	Effect	Δscore
11:10857988:G:C	donor_gain	1.0000
11:10854852:T:C	acceptor_gain	0.9900
11:10854852:T:TC	acceptor_gain	0.9900
11:10855088:T:C	acceptor_gain	0.9900
11:10855106:A:C	acceptor_gain	0.9900
11:10854846:A:AC	acceptor_gain	0.9800
11:10855099:T:TC	acceptor_gain	0.9800
11:10855103:C:CT	acceptor_gain	0.9800
11:10857082:T:TA	donor_gain	0.9800
11:10857683:CCAA:C	donor_gain	0.9800
11:10857684:CAAC:C	donor_gain	0.9800
11:10857685:AACA:A	donor_gain	0.9800
11:10857040:AAAGC:A	donor_gain	0.9700
11:10857985:T:A	donor_gain	0.9700
11:10854845:A:T	acceptor_gain	0.9600
11:10855082:CTTTT:C	acceptor_gain	0.9600
11:10857300:C:CA	donor_gain	0.9600
11:10854844:CAA:C	acceptor_gain	0.9500
11:10855087:C:CC	acceptor_gain	0.9500
11:10858005:AGG:A	donor_gain	0.9500
11:10854838:C:CT	acceptor_gain	0.9400
11:10854838:C:T	acceptor_gain	0.9400
11:10854911:T:TC	acceptor_gain	0.9400
11:10855119:C:CC	acceptor_gain	0.9400
11:10856256:GCC:G	acceptor_loss	0.9400
11:10856257:CCTAG:C	acceptor_loss	0.9400
11:10856258:CTAG:C	acceptor_loss	0.9400
11:10856259:T:G	acceptor_loss	0.9400
11:10857659:G:GT	donor_gain	0.9400
11:10855105:C:CT	acceptor_gain	0.9300

AlphaMissense

4572 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:10854589:A:C	F119L	0.996
11:10854589:A:T	F119L	0.996
11:10854591:A:G	F119L	0.996
11:10854590:A:G	F119S	0.988
11:10854445:A:C	F167L	0.983
11:10854445:A:T	F167L	0.983
11:10854447:A:G	F167L	0.983
11:10854497:C:G	R150P	0.980
11:10854442:G:C	F168L	0.978
11:10854442:G:T	F168L	0.978
11:10854444:A:G	F168L	0.978
11:10854490:A:C	H152Q	0.977
11:10854490:A:T	H152Q	0.977
11:10853032:A:C	F638L	0.976
11:10853032:A:T	F638L	0.976
11:10853034:A:G	F638L	0.976
11:10854360:C:G	A196P	0.975
11:10854593:C:T	G118E	0.975
11:10853098:A:C	F616L	0.974
11:10853098:A:T	F616L	0.974
11:10853100:A:G	F616L	0.974
11:10854224:A:T	V241E	0.972
11:10854127:A:C	F273L	0.971
11:10854127:A:T	F273L	0.971
11:10854129:A:G	F273L	0.971
11:10853212:A:C	F578L	0.970
11:10853212:A:T	F578L	0.970
11:10853214:A:G	F578L	0.970
11:10854197:C:G	R250P	0.968
11:10854282:C:G	A222P	0.967

dbSNP variants (sampled 300 via entrez): RS1000210877 (11:10852625 C>T), RS1000595629 (11:10858274 G>C), RS1000718328 (11:10852422 A>C), RS1000967628 (11:10858456 G>A), RS1001709153 (11:10858878 A>G), RS1001878211 (11:10852531 G>C), RS1002138066 (11:10857394 G>T), RS1002138935 (11:10858736 C>T), RS1002320563 (11:10858281 T>G), RS1002584755 (11:10855898 T>A), RS1002963861 (11:10856315 G>A), RS1003087984 (11:10856219 A>C), RS1003549977 (11:10855983 A>G), RS1003558771 (11:10854718 T>C), RS1003577252 (11:10859983 C>T)

Disease associations

OMIM: gene MIM:615251 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003820_3	Knee osteoarthritis	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs10840501	ZBED5		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
trichostatin A	affects expression	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
jinfukang	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Atrazine	decreases expression	1
Vehicle Emissions	increases abundance, increases expression	1
Carbamazepine	affects expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Naled	affects expression	1
Ozone	affects expression, increases abundance	1
Quercetin	decreases expression	1
Silver	decreases expression	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

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