ZBED11

Summary

ZBED11 (zinc finger BED-type containing 11, HGNC:27740) is a protein-coding gene on chromosome 4p15.32, encoding Protein FAM200B (P0CF97).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001145191

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27740
Approved symbol	ZBED11
Name	zinc finger BED-type containing 11
Location	4p15.32
Locus type	gene with protein product
Status	Approved
Aliases	C4orf53
Ensembl gene	ENSG00000237765
Ensembl biotype	protein_coding
Entrez	285550

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 15 protein_coding_CDS_not_defined, 9 protein_coding

ENST00000422728, ENST00000502502, ENST00000502856, ENST00000503600, ENST00000503617, ENST00000504137, ENST00000504823, ENST00000505260, ENST00000506610, ENST00000507305, ENST00000507992, ENST00000508567, ENST00000509022, ENST00000510032, ENST00000510186, ENST00000510920, ENST00000512855, ENST00000513053, ENST00000514803, ENST00000515430, ENST00000515697, ENST00000859508, ENST00000859509, ENST00000926146

RefSeq mRNA: 1 — MANE Select: NM_001145191 NM_001145191

CCDS: CCDS47028

Canonical transcript exons

ENST00000422728 — 2 exons

Exon	Start	End
ENSE00001736652	15686236	15690447
ENSE00002069002	15681827	15681901

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 97.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 50.8779 / max 315.7795, expressed in 1819 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46995	35.4776	1799
46994	6.0813	1621
46993	4.5753	1505
46990	3.1926	694
46992	1.3364	529
46991	0.2147	117

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	97.27	gold quality
leukocyte	CL:0000738	97.05	gold quality
cortical plate	UBERON:0005343	95.83	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	95.59	gold quality
sperm	CL:0000019	95.56	gold quality
adenohypophysis	UBERON:0002196	95.21	gold quality
calcaneal tendon	UBERON:0003701	95.15	gold quality
ganglionic eminence	UBERON:0004023	94.87	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.61	gold quality
lower esophagus	UBERON:0013473	94.58	gold quality
nucleus accumbens	UBERON:0001882	94.42	gold quality
caudate nucleus	UBERON:0001873	94.26	gold quality
putamen	UBERON:0001874	94.26	gold quality
anterior cingulate cortex	UBERON:0009835	94.25	gold quality
pituitary gland	UBERON:0000007	94.24	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.04	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.99	gold quality
hypothalamus	UBERON:0001898	93.93	gold quality
prefrontal cortex	UBERON:0000451	93.79	gold quality
left ovary	UBERON:0002119	93.73	gold quality
amygdala	UBERON:0001876	93.70	gold quality
spinal cord	UBERON:0002240	93.62	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.60	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.26	gold quality
metanephros cortex	UBERON:0010533	93.20	gold quality
mucosa of stomach	UBERON:0001199	93.19	gold quality
right coronary artery	UBERON:0001625	93.14	gold quality
left adrenal gland cortex	UBERON:0035825	93.14	gold quality
left lobe of thyroid gland	UBERON:0001120	93.08	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-124858	no	231.57
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2588.1	FAM200B	BED zinc finger factors

JASPAR matrix evidence (PMIDs): PMID:39605320

miRNA regulators (miRDB)

87 targeting ZBED11, 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-3064-3P	100.00	70.09	1254
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502

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), ZBED5 (ENSG00000236287), GTF2I (ENSG00000263001)

Protein

Protein identifiers

Protein FAM200B — P0CF97 (reviewed: P0CF97)

All UniProt accessions (5): P0CF97, A0A6Q8PFA1, A0A6Q8PG77, A0A6Q8PGG8, D6RAC6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM200 family.

RefSeq proteins (1): NP_001138663* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012337	RNaseH-like_sf	Homologous_superfamily

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CF97-F1	81.06	0.51

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, chr4p15, HORIUCHI_WTAP_TARGETS_UP, ARHGAP35_TARGET_GENES, ARNT2_TARGET_GENES, BANP_TARGET_GENES, DYRK1A_TARGET_GENES, E2F2_TARGET_GENES, E2F5_TARGET_GENES, HMGA1_TARGET_GENES, HSD17B8_TARGET_GENES, IRF5_TARGET_GENES, KLF7_TARGET_GENES, MSX1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

192 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZBED11	C1orf50	Q9BV19	506
ZBED11	OR5P2	Q8WZ92	477
ZBED11	GOLGA6L10	A6NI86	477
ZBED11	SUGP2	Q8IX01	462
ZBED11	ANKRD45	Q5TZF3	433
ZBED11	C1orf198	Q9H425	432
ZBED11	DEF8	Q6ZN54	430
ZBED11	TMEM120A	Q9BXJ8	429
ZBED11	NAGPA	Q9UK23	423
ZBED11	C14orf132	Q9NPU4	417
ZBED11	FAM133A	Q8N9E0	375
ZBED11	BTBD10	Q9BSF8	375
ZBED11	GARIN5B	Q8N5Q1	360
ZBED11	H3BVE0	H3BVE0	358
ZBED11	BRINP2	Q9C0B6	348

IntAct

2 interactions, top by confidence:

A	B	Type	Score
FAM200A	FAM200B	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): FAM200B (Affinity Capture-RNA), FAM200B (Affinity Capture-MS), FAM200B (Affinity Capture-MS), FAM200B (Cross-Linking-MS (XL-MS)), FAM200B (Protein-peptide)

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

773 predictions. Top by Δscore:

Variant	Effect	Δscore
4:15686999:A:G	acceptor_gain	0.9900
4:15684849:GCCAA:G	acceptor_gain	0.9700
4:15686230:TCCCA:T	acceptor_loss	0.9700
4:15686231:CCCAG:C	acceptor_loss	0.9700
4:15686232:CCA:C	acceptor_loss	0.9700
4:15686233:CA:C	acceptor_loss	0.9700
4:15686234:A:AT	acceptor_loss	0.9700
4:15686235:G:GA	acceptor_loss	0.9700
4:15686358:A:T	donor_gain	0.9700
4:15686357:G:GT	donor_gain	0.9600
4:15687000:G:GG	acceptor_gain	0.9600
4:15686372:A:G	donor_gain	0.9500
4:15681781:TGAGG:T	donor_loss	0.9400
4:15681782:GAGGT:G	donor_loss	0.9400
4:15681783:AGGT:A	donor_loss	0.9400
4:15681784:GGTAG:G	donor_loss	0.9400
4:15681786:T:G	donor_loss	0.9400
4:15686234:A:AG	acceptor_gain	0.9400
4:15686235:G:GG	acceptor_gain	0.9400
4:15684848:A:AG	acceptor_gain	0.9200
4:15684849:G:GG	acceptor_gain	0.9200
4:15686924:T:TA	acceptor_gain	0.9200
4:15681967:GG:G	donor_gain	0.9100
4:15681968:GG:G	donor_gain	0.9100
4:15686925:GAGT:G	acceptor_gain	0.9100
4:15686923:TTGAG:T	acceptor_gain	0.9000
4:15686924:TGAG:T	acceptor_gain	0.9000
4:15681811:G:T	donor_gain	0.8900
4:15684884:A:G	acceptor_gain	0.8900
4:15686927:GTTA:G	acceptor_gain	0.8900

AlphaMissense

4368 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:15687191:T:C	F72L	0.979
4:15687193:T:A	F72L	0.979
4:15687193:T:G	F72L	0.979
4:15687341:T:C	F122L	0.934
4:15687343:T:A	F122L	0.934
4:15687343:T:G	F122L	0.934
4:15687285:T:C	L103S	0.924
4:15688790:T:C	F605L	0.921
4:15688792:C:A	F605L	0.921
4:15688792:C:G	F605L	0.921
4:15688724:T:C	F583L	0.917
4:15688726:T:A	F583L	0.917
4:15688726:T:G	F583L	0.917
4:15688598:T:C	F541L	0.915
4:15688600:T:A	F541L	0.915
4:15688600:T:G	F541L	0.915
4:15687192:T:C	F72S	0.911
4:15687650:T:C	F225L	0.906
4:15687652:T:A	F225L	0.906
4:15687652:T:G	F225L	0.906
4:15687295:C:A	H106Q	0.875
4:15687295:C:G	H106Q	0.875
4:15687237:T:A	V87D	0.874
4:15688769:A:C	S598R	0.868
4:15688771:T:A	S598R	0.868
4:15688771:T:G	S598R	0.868
4:15688427:T:C	F484L	0.866
4:15688429:T:A	F484L	0.866
4:15688429:T:G	F484L	0.866
4:15687274:A:C	K99N	0.864

dbSNP variants (sampled 300 via entrez): RS1000151274 (4:15656957 G>A), RS1000222190 (4:15658403 A>G), RS1000231753 (4:15670201 T>C), RS1000296650 (4:15640194 C>T), RS1000304078 (4:15655730 G>A), RS1000412343 (4:15639919 A>C), RS1000418538 (4:15656613 T>C), RS10005158 (4:15649651 G>A), RS1000576258 (4:15662056 G>T), RS1000628361 (4:15687730 TGATTTTTTGGAG>T), RS1000689673 (4:15675565 A>G), RS1000741339 (4:15652240 CAGG>C), RS1000781231 (4:15663795 G>A), RS1000832848 (4:15669877 T>A), RS1000834149 (4:15681548 G>A,T)

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

1 associations (top):

Study	Trait	p-value
GCST004902_46	Parkinson’s disease	1.000000e-19

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression	6
trichostatin A	affects cotreatment, decreases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Particulate Matter	increases abundance, decreases expression	2
aristolochic acid I	increases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
potassium chromate(VI)	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
monomethylarsonous acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	increases expression, affects cotreatment	1
Temozolomide	decreases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Vehicle Emissions	increases abundance, decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1

Clinical trials (associated diseases)

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