ZBED8

Summary

ZBED8 (zinc finger BED-type containing 8, HGNC:30804) is a protein-coding gene on chromosome 5q33.3, encoding Protein FAM200C (Q8IZ13).

Located in nucleoplasm.

Source: NCBI Gene 63920 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_022090

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30804
Approved symbol	ZBED8
Name	zinc finger BED-type containing 8
Location	5q33.3
Locus type	gene with protein product
Status	Approved
Aliases	Buster3
Ensembl gene	ENSG00000221886
Ensembl biotype	protein_coding
OMIM	615253
Entrez	63920

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000408953, ENST00000523213, ENST00000929527, ENST00000929528, ENST00000944851, ENST00000944852, ENST00000944853, ENST00000944854

RefSeq mRNA: 2 — MANE Select: NM_022090 NM_001303251, NM_022090

CCDS: CCDS34283

Canonical transcript exons

ENST00000408953 — 2 exons

Exon	Start	End
ENSE00001568387	160393148	160395539
ENSE00002132563	160399639	160400054

Expression profiles

Bgee: expression breadth ubiquitous, 228 present calls, max score 85.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.3701 / max 65.6686, expressed in 1417 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64629	3.2861	1261
64630	0.7562	510
64628	0.3278	168

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	85.26	gold quality
ganglionic eminence	UBERON:0004023	84.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.70	gold quality
cortical plate	UBERON:0005343	82.82	gold quality
cerebellar hemisphere	UBERON:0002245	80.61	gold quality
cerebellar cortex	UBERON:0002129	80.46	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.26	gold quality
cerebellum	UBERON:0002037	79.61	gold quality
pituitary gland	UBERON:0000007	79.54	gold quality
adenohypophysis	UBERON:0002196	79.33	gold quality
left ovary	UBERON:0002119	79.20	gold quality
embryo	UBERON:0000922	78.30	gold quality
right ovary	UBERON:0002118	78.30	gold quality
ovary	UBERON:0000992	78.22	gold quality
endocervix	UBERON:0000458	78.05	gold quality
tibia	UBERON:0000979	77.96	gold quality
right coronary artery	UBERON:0001625	77.78	gold quality
islet of Langerhans	UBERON:0000006	77.77	gold quality
germinal epithelium of ovary	UBERON:0001304	77.74	gold quality
popliteal artery	UBERON:0002250	77.41	gold quality
descending thoracic aorta	UBERON:0002345	77.40	gold quality
blood vessel layer	UBERON:0004797	77.40	gold quality
tibial artery	UBERON:0007610	77.38	gold quality
body of uterus	UBERON:0009853	77.36	gold quality
bronchial epithelial cell	CL:0002328	77.10	gold quality
aorta	UBERON:0000947	76.83	gold quality
right uterine tube	UBERON:0001302	76.75	gold quality
calcaneal tendon	UBERON:0003701	76.67	gold quality
ascending aorta	UBERON:0001496	76.34	gold quality
thoracic aorta	UBERON:0001515	76.30	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.44
E-MTAB-6678	no	2.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting ZBED8, 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-1277-5P	100.00	73.95	5056
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-34B-5P	99.78	67.56	1175
HSA-MIR-449C-5P	99.78	67.63	1168
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-2682-5P	99.73	67.38	1055
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-6080	99.43	69.43	373
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-1264	99.25	66.81	1317
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-877-3P	99.09	68.10	1637
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-4477A	98.83	69.75	2952

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), FAM200A (ENSG00000221909), SCAND3 (ENSG00000232040), ZBED5 (ENSG00000236287), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Protein

Protein identifiers

Protein FAM200C — Q8IZ13 (reviewed: Q8IZ13)

Alternative names: Protein ZBED8, Transposon-derived Buster3 transposase-like protein, Zinc finger BED domain-containing protein 8

All UniProt accessions (1): Q8IZ13

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be derived from an ancient transposon that has lost its ability to translocate. Exhibits a close evolutionary relationship with ZBED5, but does not contain any zinc finger.

RefSeq proteins (2): NP_001290180, NP_071373* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012337	RNaseH-like_sf	Homologous_superfamily

UniProt features (5 total): sequence conflict 3, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IZ13-F1	82.40	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 64 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN, CHEN_HOXA5_TARGETS_6HR_DN, MODULE_301, NUYTTEN_EZH2_TARGETS_DN, NAGASHIMA_NRG1_SIGNALING_DN, KIM_WT1_TARGETS_DN, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, MODULE_49, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, SMIRNOV_RESPONSE_TO_IR_2HR_DN, MTOR_UP.N4.V1_DN, SHEN_SMARCA2_TARGETS_UP, E2F2_TARGET_GENES, FOXG1_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

254 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZBED8	PGBD2	Q6P3X8	617
ZBED8	ZNF862	O60290	498
ZBED8	POGK	Q9P215	498
ZBED8	PGBD5	Q8N414	478
ZBED8	THAP9	Q9H5L6	477
ZBED8	GIN1	Q9NXP7	477
ZBED8	PGBD1	Q96JS3	466
ZBED8	NAIF1	Q69YI7	460
ZBED8	ZBED10P	Q96FA7	447
ZBED8	TTC33	Q6PID6	434
ZBED8	HARBI1	Q96MB7	433
ZBED8	NYNRIN	Q9P2P1	433
ZBED8	AIRIM	Q9NX04	432
ZBED8	KIAA1586	Q9HCI6	396
ZBED8	ASPHD2	Q6ICH7	395

IntAct

40 interactions, top by confidence:

A	B	Type	Score
NAB2	FAM200C	psi-mi:“MI:0915”(physical association)	0.780
METTL21A	FAM200C	psi-mi:“MI:0915”(physical association)	0.740
FAM200C	METTL21A	psi-mi:“MI:0915”(physical association)	0.740
FAM200C	ARP2	psi-mi:“MI:0915”(physical association)	0.560
ARP2	FAM200C	psi-mi:“MI:0915”(physical association)	0.560
REL	FAM200C	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	FAM200C	psi-mi:“MI:0915”(physical association)	0.560
FAM200C	DDIT4L	psi-mi:“MI:0915”(physical association)	0.560
FAM200C	CRLF3	psi-mi:“MI:0914”(association)	0.530
ANKRD22	ESYT2	psi-mi:“MI:0914”(association)	0.530
FAM200C	EED	psi-mi:“MI:0915”(physical association)	0.370
EEF1G	FAM200C	psi-mi:“MI:0915”(physical association)	0.370
FAM200C	HSF4	psi-mi:“MI:0915”(physical association)	0.370
FAM200C	CEP126	psi-mi:“MI:0915”(physical association)	0.370
FAM200C	MBTPS1	psi-mi:“MI:0915”(physical association)	0.370
Lck	TLE5	psi-mi:“MI:0914”(association)	0.350
APLNR	TTI1	psi-mi:“MI:0914”(association)	0.350
CD80	RIMOC1	psi-mi:“MI:0914”(association)	0.350
VSIG1	RIMOC1	psi-mi:“MI:0914”(association)	0.350
FAM200C	REL	psi-mi:“MI:0915”(physical association)	0.000
METTL21A	FAM200C	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (23): ZBED8 (Two-hybrid), ZBED8 (Affinity Capture-RNA), ZBED8 (Two-hybrid), ZBED8 (Affinity Capture-MS), CRLF3 (Affinity Capture-MS), ZNF507 (Affinity Capture-MS), ARNTL2 (Affinity Capture-MS), ARID3A (Affinity Capture-MS), ZBED8 (Two-hybrid), ZBED8 (Two-hybrid), ZBED8 (Two-hybrid), ZBED8 (Two-hybrid), ZBED8 (Two-hybrid), ZBED8 (Two-hybrid), ZNF507 (Affinity Capture-MS)

ESM2 similar proteins: A4IFA3, A4Z943, A4Z944, A4Z945, B2RRL2, D3Z4R1, F1NQJ3, O43422, O60108, O60290, O96006, P08770, P0CF97, P12258, P16320, P34601, Q09772, Q0VBL1, Q17RP2, Q3EBC8, Q3YK19, Q49AG3, Q4R6P1, Q4W5G0, Q5SVZ6, Q5SXJ3, Q6EKJ0, Q6NT04, Q6R2W3, Q7L775, Q7M3K2, Q86UP8, Q8BUZ3, Q8IY51, Q8IZ13, Q8TBB0, Q8TCP9, Q8TDG4, Q8VEH5, Q95M72

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

339 predictions. Top by Δscore:

Variant	Effect	Δscore
5:160399699:A:C	donor_gain	1.0000
5:160399801:G:C	donor_gain	0.9900
5:160399861:T:TA	donor_gain	0.9900
5:160399897:T:A	donor_gain	0.9900
5:160399904:AG:A	donor_gain	0.9900
5:160399909:AGGG:A	donor_gain	0.9900
5:160399909:AGGGC:A	donor_gain	0.9900
5:160399721:A:AC	donor_gain	0.9800
5:160399722:C:CC	donor_gain	0.9800
5:160399905:G:C	donor_gain	0.9800
5:160400017:T:TA	donor_gain	0.9800
5:160395535:TTTTG:T	acceptor_gain	0.9700
5:160395542:T:C	acceptor_gain	0.9700
5:160399800:A:AC	donor_gain	0.9700
5:160399800:AGCG:A	donor_gain	0.9700
5:160399928:TCGGA:T	donor_gain	0.9700
5:160395540:C:CC	acceptor_gain	0.9600
5:160395542:T:TC	acceptor_gain	0.9600
5:160399800:AG:A	donor_gain	0.9600
5:160399916:AG:A	donor_gain	0.9500
5:160398404:G:C	donor_gain	0.9400
5:160399855:CGGG:C	donor_gain	0.9400
5:160399867:AGGCG:A	donor_gain	0.9400
5:160395537:TTG:T	acceptor_gain	0.9300
5:160395541:T:C	acceptor_gain	0.9300
5:160399951:T:TA	donor_gain	0.9300
5:160395536:TTTG:T	acceptor_gain	0.9200
5:160400063:T:TA	donor_gain	0.9200
5:160395538:TG:T	acceptor_gain	0.9000
5:160400005:T:TA	donor_gain	0.9000

AlphaMissense

3982 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:160395443:G:C	F16L	0.991
5:160395443:G:T	F16L	0.991
5:160395445:A:G	F16L	0.991
5:160395444:A:G	F16S	0.969
5:160393877:A:C	F538L	0.963
5:160393877:A:T	F538L	0.963
5:160393879:A:G	F538L	0.963
5:160393943:G:C	F516L	0.957
5:160393943:G:T	F516L	0.957
5:160393945:A:G	F516L	0.957
5:160393919:A:C	F524L	0.951
5:160393919:A:T	F524L	0.951
5:160393921:A:G	F524L	0.951
5:160395341:A:C	H50Q	0.944
5:160395341:A:T	H50Q	0.944
5:160394918:A:C	F191L	0.942
5:160394918:A:T	F191L	0.942
5:160394920:A:G	F191L	0.942
5:160395121:C:G	A124P	0.941
5:160393967:A:C	F508L	0.932
5:160393967:A:T	F508L	0.932
5:160393969:A:G	F508L	0.932
5:160395111:A:T	V127D	0.924
5:160394057:A:C	F478L	0.922
5:160394057:A:T	F478L	0.922
5:160394059:A:G	F478L	0.922
5:160394074:A:G	W473R	0.921
5:160394074:A:T	W473R	0.921
5:160394987:A:C	S168R	0.919
5:160394987:A:T	S168R	0.919

dbSNP variants (sampled 300 via entrez): RS1000234097 (5:160401617 A>G), RS1000465140 (5:160402005 A>T), RS1001017048 (5:160399223 A>T), RS1001611935 (5:160395341 A>G), RS1002214961 (5:160397165 A>T), RS1002486039 (5:160396228 T>C), RS1002588530 (5:160396851 G>T), RS1003255666 (5:160393636 GAGAC>G), RS1003457159 (5:160397529 A>G), RS1004159191 (5:160397230 C>T), RS1004256824 (5:160396292 T>C), RS1004455078 (5:160396750 C>A,G), RS1004516632 (5:160401844 A>G), RS1004652537 (5:160401503 G>A,C), RS10058931 (5:160398378 C>A,T)

Disease associations

OMIM: gene MIM:615253 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	6
Benzo(a)pyrene	affects methylation, decreases expression, increases expression	4
trichostatin A	affects cotreatment, decreases expression	2
Estradiol	decreases expression, increases expression	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	decreases expression	2
Cyclosporine	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
bisphenol F	affects cotreatment, increases methylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
deoxynivalenol	increases expression	1
tributyltin	increases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
dibutyldichlorotin	increases expression	1
manganese chloride	increases abundance, increases expression	1
2-palmitoylglycerol	increases 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	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Fingolimod Hydrochloride	increases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Amphotericin B	decreases expression	1

Clinical trials (associated diseases)

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