ZNF239

Summary

ZNF239 (zinc finger protein 239, HGNC:13031) is a protein-coding gene on chromosome 10q11.21, encoding Zinc finger protein 239 (Q16600). May be involved in transcriptional regulation.

MOK2 proteins are DNA- and RNA-binding proteins that are mainly associated with nuclear RNP components, including the nucleoli and extranucleolar structures (Arranz et al., 1997 [PubMed 9121460]).

Source: NCBI Gene 8187 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_001099282

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13031
Approved symbol	ZNF239
Name	zinc finger protein 239
Location	10q11.21
Locus type	gene with protein product
Status	Approved
Aliases	MOK2, HOK-2
Ensembl gene	ENSG00000196793
Ensembl biotype	protein_coding
OMIM	601069
Entrez	8187

Gene structure

Transcript identifiers

Ensembl transcripts: 50 — 49 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000306006, ENST00000374446, ENST00000426961, ENST00000491188, ENST00000535642, ENST00000886909, ENST00000886910, ENST00000886911, ENST00000886912, ENST00000886913, ENST00000886914, ENST00000886915, ENST00000886916, ENST00000886917, ENST00000886918, ENST00000886919, ENST00000886920, ENST00000886921, ENST00000886922, ENST00000886923, ENST00000886924, ENST00000886925, ENST00000924061, ENST00000924062, ENST00000924063, ENST00000924064, ENST00000924065, ENST00000924066, ENST00000924067, ENST00000924068, ENST00000924069, ENST00000924070, ENST00000924071, ENST00000924072, ENST00000924073, ENST00000924074, ENST00000924075, ENST00000924076, ENST00000924077, ENST00000924078, ENST00000924079, ENST00000924080, ENST00000924081, ENST00000924082, ENST00000943655, ENST00000943656, ENST00000943657, ENST00000943658, ENST00000943659, ENST00000943660

RefSeq mRNA: 11 — MANE Select: NM_001099282 NM_001099282, NM_001099283, NM_001099284, NM_001324347, NM_001324348, NM_001324349, NM_001324350, NM_001324351, NM_001324352, NM_001324353, NM_005674

CCDS: CCDS41502

Canonical transcript exons

ENST00000374446 — 4 exons

Exon	Start	End
ENSE00001400132	43573637	43573677
ENSE00001433467	43567899	43568021
ENSE00001463532	43556344	43558171
ENSE00001463534	43574540	43574616

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 89.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.7431 / max 54.1666, expressed in 1109 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
109181	2.7431	1109

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.03	gold quality
endothelial cell	CL:0000115	88.60	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.17	gold quality
cortical plate	UBERON:0005343	83.49	gold quality
ganglionic eminence	UBERON:0004023	78.42	gold quality
ventricular zone	UBERON:0003053	78.41	gold quality
body of pancreas	UBERON:0001150	75.21	gold quality
islet of Langerhans	UBERON:0000006	73.92	gold quality
pancreas	UBERON:0001264	73.79	gold quality
stromal cell of endometrium	CL:0002255	73.52	gold quality
prefrontal cortex	UBERON:0000451	73.05	gold quality
smooth muscle tissue	UBERON:0001135	72.88	gold quality
pancreatic ductal cell	CL:0002079	72.83	gold quality
right testis	UBERON:0004534	72.54	gold quality
testis	UBERON:0000473	72.53	gold quality
left testis	UBERON:0004533	72.51	gold quality
body of uterus	UBERON:0009853	72.12	gold quality
gastrocnemius	UBERON:0001388	72.09	gold quality
muscle of leg	UBERON:0001383	71.82	gold quality
lower esophagus muscularis layer	UBERON:0035833	71.71	gold quality
adenohypophysis	UBERON:0002196	71.66	gold quality
lower esophagus	UBERON:0013473	71.64	gold quality
middle temporal gyrus	UBERON:0002771	71.56	silver quality
right coronary artery	UBERON:0001625	71.51	gold quality
popliteal artery	UBERON:0002250	71.47	gold quality
tibial artery	UBERON:0007610	71.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	71.42	gold quality
epithelial cell of pancreas	CL:0000083	71.31	silver quality
thoracic aorta	UBERON:0001515	71.29	gold quality
endocervix	UBERON:0000458	71.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.54

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

Target	Regulation
GRB10
RBP3	Repression

miRNA regulators (miRDB)

57 targeting ZNF239, 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-340-5P	100.00	72.50	4437
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-6845-3P	99.94	66.88	1439
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-548AQ-5P	99.94	71.34	3426
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
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-30A-3P	99.87	69.74	2928

Literature-anchored findings (GeneRIF, showing 3)

• In this study, we identify a novel interaction between lamin A/C and hsMOK2 by using the yeast two-hybrid system (PMID:12409453)
• Results indicate that pathogenic mutations in lamin A/C lead to sequestration of hsMOK2 into nuclear aggregates, which may deregulate MOK2 target genes. (PMID:17760566)
• Data identified Ser38 and Ser129 of hsMOK2 as phosphorylation sites of JNK3 kinase, and Ser46 as a phosphorylation site of Aurora A and protein kinase A. (PMID:19490114)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp239	ENSMUSG00000042097
rattus_norvegicus	Zfp239	ENSRNOG00000062429

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 239 — Q16600 (reviewed: Q16600)

Alternative names: Zinc finger protein HOK-2, Zinc finger protein MOK-2

All UniProt accessions (1): Q16600

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

RefSeq proteins (11): NP_001092752, NP_001092753, NP_001092754, NP_001311276, NP_001311277, NP_001311278, NP_001311279, NP_001311280, NP_001311281, NP_001311282, NP_005665 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (17 total): zinc finger region 9, sequence variant 3, sequence conflict 2, chain 1, modified residue 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q16600-F1	63.02	0.40

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 (2): 191, 108

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 134 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, SCHUHMACHER_MYC_TARGETS_UP, LIAO_METASTASIS, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN, MORF_RAB3A, ZHANG_BREAST_CANCER_PROGENITORS_UP, MORF_WNT1, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, MORF_IL9, GOCC_NUCLEAR_BODY, DANG_REGULATED_BY_MYC_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MIKKELSEN_ES_ICP_WITH_H3K4ME3

GO Biological Process (3): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), regulation of gene expression (GO:0010468)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA binding (GO:0003677), RNA binding (GO:0003723), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
nucleic acid binding	2
negative regulation of DNA-templated transcription	1
regulation of DNA-templated transcription	1
gene expression	1
regulation of macromolecule biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

466 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF239	RBP3	P10745	884
ZNF239	LMNA	P02545	788
ZNF239	PAX3	P23760	690
ZNF239	LMNB1	P20700	552
ZNF239	LMNB2	Q03252	538
ZNF239	E9PCK9	E9PCK9	447
ZNF239	MRPL14	Q6P1L8	447
ZNF239	FOS	P01100	424
ZNF239	EMD	P50402	420
ZNF239	RAB17	Q9H0T7	418
ZNF239	CLLU1-AS1	Q5K130	392
ZNF239	C2orf15	Q8WU43	391
ZNF239	ARID3A	Q99856	368
ZNF239	LBR	Q14739	368
ZNF239	RIBC2	Q9H4K1	367

IntAct

32 interactions, top by confidence:

A	B	Type	Score
ZNF239	CEP70	psi-mi:“MI:0915”(physical association)	0.720
CEP70	ZNF239	psi-mi:“MI:0915”(physical association)	0.720
ZNF239	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-6	ZNF239	psi-mi:“MI:0915”(physical association)	0.560
ZNF239	CARD10	psi-mi:“MI:0915”(physical association)	0.560
WTAP	ZNF239	psi-mi:“MI:0915”(physical association)	0.560
ZNF239	GRN	psi-mi:“MI:0915”(physical association)	0.560
ZNF239	WFS1	psi-mi:“MI:0915”(physical association)	0.560
ZNF239	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
M		psi-mi:“MI:0914”(association)	0.350
SLC1A3	DDX11L8	psi-mi:“MI:0914”(association)	0.350
SLC30A6	PSMD14	psi-mi:“MI:0914”(association)	0.350
	EBAG9	psi-mi:“MI:0914”(association)	0.350
ZNF239	CEP70	psi-mi:“MI:0915”(physical association)	0.000
MTUS2	ZNF239	psi-mi:“MI:0915”(physical association)	0.000
ZNF239	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.000
ZNF239	MTUS2	psi-mi:“MI:0915”(physical association)	0.000
ZNF239	CARD10	psi-mi:“MI:0915”(physical association)	0.000
ZNF239	WTAP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (36): CEP70 (Two-hybrid), ZNF239 (Affinity Capture-MS), ZNF239 (Two-hybrid), ZNF239 (Two-hybrid), ZNF239 (Two-hybrid), ZNF239 (Two-hybrid), ZNF239 (Two-hybrid), ZNF239 (Two-hybrid), ZNF239 (Reconstituted Complex), ZNF239 (Affinity Capture-MS), ZNF239 (Affinity Capture-MS), ZNF239 (Affinity Capture-MS), ZNF239 (Affinity Capture-MS), ZNF239 (Affinity Capture-MS), ZNF239 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

Diamond homologs: Q16600, Q5R8G9

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ZNF239	“down-regulates quantity by repression”	RBP3	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

386 predictions. Top by Δscore:

Variant	Effect	Δscore
10:43558169:CTC:C	acceptor_gain	0.9800
10:43558170:TC:T	acceptor_gain	0.9800
10:43558171:CC:C	acceptor_gain	0.9800
10:43558172:C:CC	acceptor_gain	0.9800
10:43558167:GTCTC:G	acceptor_gain	0.9700
10:43558170:TCCTA:T	acceptor_loss	0.9700
10:43558172:C:CA	acceptor_loss	0.9700
10:43558173:T:A	acceptor_loss	0.9700
10:43567946:T:TA	donor_gain	0.9300
10:43558180:C:CT	acceptor_gain	0.9200
10:43559539:G:GA	donor_gain	0.9200
10:43567893:AC:A	donor_gain	0.9000
10:43567894:CC:C	donor_gain	0.9000
10:43567894:CCCA:C	donor_gain	0.8900
10:43568386:CATTT:C	donor_gain	0.8700
10:43568364:T:C	donor_gain	0.8200
10:43567893:A:AC	donor_gain	0.8100
10:43567894:C:CC	donor_gain	0.8100
10:43566889:A:AC	donor_gain	0.8000
10:43566890:C:CC	donor_gain	0.8000
10:43558168:TCTC:T	acceptor_gain	0.7900
10:43558169:CTCC:C	acceptor_gain	0.7900
10:43558170:TCCT:T	acceptor_gain	0.7900
10:43567889:CCTT:C	donor_loss	0.7900
10:43567890:CTTA:C	donor_loss	0.7900
10:43567891:TTAC:T	donor_loss	0.7900
10:43567892:T:TA	donor_loss	0.7900
10:43567893:A:AA	donor_loss	0.7900
10:43567894:C:CG	donor_loss	0.7900
10:43568394:AATCT:A	donor_gain	0.7900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000296369 (10:43562506 G>A), RS1000340574 (10:43575542 G>C), RS1000374779 (10:43575906 G>A), RS1000667401 (10:43569697 T>C), RS1000975917 (10:43571342 T>G), RS1000994681 (10:43564254 G>A,C), RS1001300195 (10:43560849 A>G), RS1001344146 (10:43566440 C>T), RS1001363328 (10:43560408 G>A), RS1001364546 (10:43574452 C>G,T), RS1001395606 (10:43574595 C>G), RS1001574292 (10:43567754 C>T), RS1001664850 (10:43561229 A>G), RS1002000296 (10:43562823 C>T), RS1002239556 (10:43567247 G>A)

Disease associations

OMIM: gene MIM:601069 | 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

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

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases expression, affects expression, increases abundance	3
sodium arsenite	decreases expression	2
Estradiol	increases expression	2
Tretinoin	decreases expression	2
Valproic Acid	affects expression, increases expression	2
aristolochic acid I	decreases expression	1
Esketamine	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	increases expression	1
arsenite	increases methylation	1
ferrous chloride	decreases expression	1
nickel sulfate	decreases expression	1
diallyl trisulfide	increases expression	1
beta-methylcholine	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
2-palmitoylglycerol	increases expression	1
nutlin 3	affects cotreatment, increases expression	1
ICG 001	increases expression	1
Temozolomide	increases expression	1
Acetaminophen	increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cisplatin	increases expression	1
Coal	increases abundance, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Hydrogen Peroxide	affects expression	1
Ozone	increases abundance, affects expression	1
Silicon Dioxide	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_HD15	HEK293 eGFP-ZNF239	Transformed cell line	Female

Clinical trials (associated diseases)

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