ZNF200

Summary

ZNF200 (zinc finger protein 200, HGNC:12993) is a protein-coding gene on chromosome 16p13.3, encoding Zinc finger protein 200 (P98182). Localizes protein arginine N-methyltransferase PRMT3 to the nucleus.

Predicted to enable zinc ion binding activity. Involved in protein localization to nucleus. Located in nucleus.

Source: NCBI Gene 7752 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 77 total
• MANE Select transcript: NM_198088

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12993
Approved symbol	ZNF200
Name	zinc finger protein 200
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000010539
Ensembl biotype	protein_coding
OMIM	603231
Entrez	7752

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 22 protein_coding, 3 retained_intron

ENST00000396868, ENST00000396870, ENST00000396871, ENST00000414144, ENST00000431561, ENST00000575285, ENST00000575617, ENST00000575630, ENST00000575948, ENST00000577015, ENST00000854056, ENST00000854057, ENST00000854058, ENST00000854059, ENST00000854060, ENST00000854061, ENST00000854062, ENST00000854063, ENST00000854064, ENST00000928466, ENST00000946755, ENST00000946756, ENST00000946757, ENST00000946758, ENST00000946759

RefSeq mRNA: 6 — MANE Select: NM_198088 NM_001145446, NM_001145447, NM_001145448, NM_003454, NM_198087, NM_198088

CCDS: CCDS10497, CCDS42112, CCDS45395

Canonical transcript exons

ENST00000414144 — 5 exons

Exon	Start	End
ENSE00000666495	3232421	3232547
ENSE00000830612	3233506	3233836
ENSE00001526551	3222325	3224613
ENSE00001626515	3234987	3235158
ENSE00003517262	3232833	3232921

Expression profiles

Bgee: expression breadth ubiquitous, 238 present calls, max score 94.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.0288 / max 91.3627, expressed in 1754 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156017	4.7915	1655
156016	1.7417	855
156015	1.4957	1007

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	94.97	gold quality
oocyte	CL:0000023	92.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.52	gold quality
sperm	CL:0000019	90.74	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.70	gold quality
male germ cell	CL:0000015	88.56	gold quality
right testis	UBERON:0004534	86.72	gold quality
left testis	UBERON:0004533	86.13	gold quality
testis	UBERON:0000473	85.62	gold quality
blood	UBERON:0000178	84.59	gold quality
granulocyte	CL:0000094	82.70	gold quality
endothelial cell	CL:0000115	82.33	gold quality
germinal epithelium of ovary	UBERON:0001304	78.40	gold quality
palpebral conjunctiva	UBERON:0001812	78.25	gold quality
placenta	UBERON:0001987	77.69	gold quality
ventricular zone	UBERON:0003053	77.48	gold quality
cortical plate	UBERON:0005343	77.13	gold quality
adrenal tissue	UBERON:0018303	76.82	gold quality
spleen	UBERON:0002106	76.73	gold quality
ganglionic eminence	UBERON:0004023	76.72	gold quality
leukocyte	CL:0000738	76.58	gold quality
periodontal ligament	UBERON:0008266	76.52	silver quality
tibia	UBERON:0000979	76.49	gold quality
monocyte	CL:0000576	76.00	gold quality
mononuclear cell	CL:0000842	75.95	gold quality
epithelium of nasopharynx	UBERON:0001951	75.92	gold quality
stromal cell of endometrium	CL:0002255	75.77	gold quality
vermiform appendix	UBERON:0001154	75.72	gold quality
parietal pleura	UBERON:0002400	74.93	gold quality
pleura	UBERON:0000977	74.63	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.09

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

94 targeting ZNF200, 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-513A-5P	100.00	69.77	2465
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881

Literature-anchored findings (GeneRIF, showing 1)

• ZNF200 is a novel binding partner of G9a. (PMID:17584299)

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-89o9.6	ENSDARG00000075639
mus_musculus	Zfp65	ENSMUSG00000071281
drosophila_melanogaster	CG9609	FBGN0030787
caenorhabditis_elegans		WBGENE00009866
caenorhabditis_elegans	M04C9.4	WBGENE00010859
caenorhabditis_elegans		WBGENE00011710
caenorhabditis_elegans		WBGENE00012969
caenorhabditis_elegans	F57C9.4	WBGENE00019011
caenorhabditis_elegans		WBGENE00019589
caenorhabditis_elegans		WBGENE00022016
caenorhabditis_elegans		WBGENE00271744

Paralogs (2): ZNF532 (ENSG00000074657), KRBOX1 (ENSG00000240747)

Protein

Protein identifiers

Zinc finger protein 200 — P98182 (reviewed: P98182)

All UniProt accessions (2): P98182, I3L1E4

UniProt curated annotations — full annotation on UniProt →

Function. Localizes protein arginine N-methyltransferase PRMT3 to the nucleus.

Subunit / interactions. Interacts (via C-terminus) with PRMT3 (via zinc-finger); the interaction is direct and required to localize protein arginine N-methyltransferase PRMT3 to the nucleus and inhibit its proteasomal degradation.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in testis, weakly expressed in spleen, thymus, prostate, ovary, small intestine colon and peripheral blood leukocytes.

Isoforms (3)

UniProt ID	Names	Canonical?
P98182-1	1	yes
P98182-2	2
P98182-3	3

RefSeq proteins (6): NP_001138918, NP_001138919, NP_001138920, NP_003445, NP_932353, NP_932354* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (12 total): zinc finger region 5, splice variant 2, region of interest 2, chain 1, sequence variant 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P98182-F1	49.89	0.10

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 102 (showing top): MORF_BRCA1, MORF_RAD51L3, YOKOE_CANCER_TESTIS_ANTIGENS, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, MODULE_397, MORF_BCL2L11, GOBP_PROTEIN_LOCALIZATION_TO_NUCLEUS, BROWNE_HCMV_INFECTION_14HR_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, MORF_RFC5, MORF_IL16, MORF_ERCC4, MARTENS_TRETINOIN_RESPONSE_DN, HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_UP, ZHANG_RESPONSE_TO_CANTHARIDIN_DN

GO Biological Process (1): protein localization to nucleus (GO:0034504)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein localization to organelle	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

630 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF200	OR1F1	O43749	854
ZNF200	EHMT2	Q96KQ7	658
ZNF200	ZNF280A	P59817	595
ZNF200	MEFV	O15553	585
ZNF200	SLC22A3	O75751	546
ZNF200	SLC22A2	O15244	543
ZNF200	TIGD7	Q6NT04	507
ZNF200	MED12	Q93074	466
ZNF200	ZNF84	P51523	462
ZNF200	ZNF382	Q96SR6	453
ZNF200	ZNF668	Q96K58	451
ZNF200	ZNF487	B1APH4	444
ZNF200	FOSB	P53539	430
ZNF200	HEY1	Q9Y5J3	429
ZNF200	ZNF738	Q8NE65	392
ZNF200	RNF2	Q99496	392

IntAct

12 interactions, top by confidence:

A	B	Type	Score
FHL2	ZNF200	psi-mi:“MI:0915”(physical association)	0.560
ZNF200	FHL2	psi-mi:“MI:0915”(physical association)	0.560
ZNF200	TASOR2	psi-mi:“MI:0915”(physical association)	0.500
ZNF200	Dlg4	psi-mi:“MI:0407”(direct interaction)	0.440
CCL1	ZNF200	psi-mi:“MI:0915”(physical association)	0.370
ZNF200	PPARGC1B	psi-mi:“MI:0915”(physical association)	0.370
ZNF200	SKIL	psi-mi:“MI:0915”(physical association)	0.370
ERH	BCLAF3	psi-mi:“MI:0914”(association)	0.350
ZNF200	ANXA13	psi-mi:“MI:0914”(association)	0.350
ZNF200	MDM2	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): FAM208B (Affinity Capture-MS), FAM208B (Affinity Capture-MS), ZNF200 (Affinity Capture-RNA), ZNF200 (Synthetic Lethality), FHL2 (Two-hybrid), ZNF200 (Affinity Capture-MS), GABPA (Affinity Capture-MS), FAM208B (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ZNF200 (Affinity Capture-MS), MDM2 (Affinity Capture-MS), ZNF200 (Two-hybrid), PPARGC1B (Two-hybrid), ZNF200 (Affinity Capture-RNA), ZNF200 (Two-hybrid)

ESM2 similar proteins: A0A0A6YYL3, A0JP26, A2A2Z9, A2RUR9, A6NC57, A6NI47, A6QR20, A8MYB1, A9JSR5, A9ZSY0, B2RU33, B7ZQJ9, F1M5M3, H3BUK9, O15050, P51954, P98182, Q19UN5, Q4UJ75, Q501X2, Q5CZ79, Q5DW34, Q5SQ80, Q5TYW2, Q5VUR7, Q66HB6, Q6NSI1, Q6S545, Q6S5H5, Q6S8J7, Q71S21, Q7TPV2, Q7TSC3, Q7ZT11, Q80X59, Q811D2, Q86Y13, Q86YR6, Q8IVF6, Q8IYA2

Diamond homologs: B0X9H6, O15090, O60315, P98182, Q6IQX8, Q7TSH3, Q8K083, Q92618, Q9H4T2, Q9P2Y4, Q9R0G7, Q62255, Q6NX45, Q86T29, Q8CF60, Q96LX8, Q9BXA9, Q9ER74, Q9NSC2, Q9NX65, Q9UL36, A1YEV9, A1YG26, A1YG60, A2ANX9, A2T712, A2T736, A2T7L7, A3KN32, A7Y7X5, B0K011, E9Q6W4, O14771, O15391, O35738, O43474, O62836, O95125, P08048, P0CG23

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	66
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

995 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3224611:CTG:C	acceptor_gain	1.0000
16:3224614:C:CC	acceptor_gain	1.0000
16:3232415:TCTTA:T	donor_loss	1.0000
16:3232416:CTTA:C	donor_loss	1.0000
16:3232417:TTACC:T	donor_loss	1.0000
16:3232418:TA:T	donor_loss	1.0000
16:3232419:A:AC	donor_gain	1.0000
16:3232419:A:C	donor_loss	1.0000
16:3232419:AC:A	donor_gain	1.0000
16:3232420:C:CC	donor_gain	1.0000
16:3232420:CC:C	donor_gain	1.0000
16:3232545:CTC:C	acceptor_gain	1.0000
16:3232546:TC:T	acceptor_gain	1.0000
16:3232547:CC:C	acceptor_gain	1.0000
16:3232548:C:CC	acceptor_gain	1.0000
16:3232548:CT:C	acceptor_loss	1.0000
16:3232828:CCCA:C	donor_loss	1.0000
16:3232829:CCA:C	donor_loss	1.0000
16:3232830:CA:C	donor_loss	1.0000
16:3232831:A:AT	donor_loss	1.0000
16:3232832:C:T	donor_loss	1.0000
16:3232918:TGCA:T	acceptor_gain	1.0000
16:3232919:GCA:G	acceptor_gain	1.0000
16:3232920:CA:C	acceptor_gain	1.0000
16:3232920:CAC:C	acceptor_gain	1.0000
16:3232921:AC:A	acceptor_loss	1.0000
16:3232922:C:CC	acceptor_gain	1.0000
16:3232922:C:CG	acceptor_loss	1.0000
16:3232923:T:A	acceptor_loss	1.0000
16:3233505:CCT:C	donor_gain	1.0000

AlphaMissense

2626 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:3224129:G:C	F317L	1.000
16:3224129:G:T	F317L	1.000
16:3224131:A:G	F317L	1.000
16:3224213:G:C	F289L	1.000
16:3224213:G:T	F289L	1.000
16:3224215:A:G	F289L	1.000
16:3224270:G:C	H270Q	1.000
16:3224270:G:T	H270Q	1.000
16:3224272:G:C	H270D	1.000
16:3224297:A:C	F261L	1.000
16:3224297:A:T	F261L	1.000
16:3224299:A:G	F261L	1.000
16:3223961:A:C	F373L	0.999
16:3223961:A:T	F373L	0.999
16:3223963:A:G	F373L	0.999
16:3224045:G:C	F345L	0.999
16:3224045:G:T	F345L	0.999
16:3224047:A:G	F345L	0.999
16:3224068:A:G	C338R	0.999
16:3224090:A:C	H330Q	0.999
16:3224090:A:T	H330Q	0.999
16:3224102:A:C	H326Q	0.999
16:3224102:A:T	H326Q	0.999
16:3224104:G:C	H326D	0.999
16:3224104:G:T	H326N	0.999
16:3224112:C:G	R323P	0.999
16:3224130:A:G	F317S	0.999
16:3224152:A:G	C310R	0.999
16:3224174:A:C	H302Q	0.999
16:3224174:A:T	H302Q	0.999

dbSNP variants (sampled 300 via entrez): RS1000144535 (16:3229527 C>A,T), RS1000326461 (16:3225056 T>C), RS1000502312 (16:3234448 G>A), RS1001046331 (16:3226130 G>A,C), RS1001072170 (16:3236807 G>C), RS1001083555 (16:3237072 A>C,G), RS1001379933 (16:3225779 C>T), RS1001539162 (16:3223469 G>C,T), RS1001690615 (16:3234678 G>A), RS1001747677 (16:3225525 T>C), RS1001967166 (16:3223589 CCA>C), RS1001983702 (16:3236729 A>G), RS1001988695 (16:3221920 A>T), RS1002009139 (16:3228033 A>C), RS1002256428 (16:3231932 G>A)

Disease associations

OMIM: gene MIM:603231 | 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

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

Chemical	Actions (top 5)	PubMed papers
Cisplatin	decreases expression, increases expression	2
Valproic Acid	affects expression, increases expression	2
Aflatoxin B1	increases methylation	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
ferrous chloride	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
motexafin gadolinium	decreases expression	1
clothianidin	decreases expression	1
abrine	increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Adenine	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases expression, increases methylation	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	increases abundance, increases expression	1
Colchicine	decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Etoposide	decreases expression	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	increases expression	1
Mitomycin	decreases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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