ZFP3

Summary

ZFP3 (ZFP3 zinc finger protein, HGNC:12861) is a protein-coding gene on chromosome 17p13.2, encoding Zinc finger protein 3 homolog (Q96NJ6). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 124961 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 55 total
• Druggable target: yes
• MANE Select transcript: NM_153018

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12861
Approved symbol	ZFP3
Name	ZFP3 zinc finger protein
Location	17p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30726, ZNF752
Ensembl gene	ENSG00000180787
Ensembl biotype	protein_coding
OMIM	194480
Entrez	124961

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000318833, ENST00000902904

RefSeq mRNA: 1 — MANE Select: NM_153018 NM_153018

CCDS: CCDS11067

Canonical transcript exons

ENST00000318833 — 2 exons

Exon	Start	End
ENSE00001278622	5078467	5078575
ENSE00001305992	5091497	5096374

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 92.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5456 / max 272.7187, expressed in 1275 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159013	6.2417	1263
159011	0.1565	71
159012	0.1474	67

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cardiac muscle of right atrium	UBERON:0003379	92.64	gold quality
epithelial cell of pancreas	CL:0000083	92.26	silver quality
left ventricle myocardium	UBERON:0006566	91.94	silver quality
bronchial epithelial cell	CL:0002328	89.50	gold quality
bronchus	UBERON:0002185	88.80	gold quality
kidney epithelium	UBERON:0004819	87.99	silver quality
germinal epithelium of ovary	UBERON:0001304	86.39	gold quality
ileal mucosa	UBERON:0000331	86.03	gold quality
secondary oocyte	CL:0000655	85.23	gold quality
tibialis anterior	UBERON:0001385	84.69	silver quality
endothelial cell	CL:0000115	84.04	silver quality
mucosa of paranasal sinus	UBERON:0005030	83.76	gold quality
epithelium of nasopharynx	UBERON:0001951	83.58	silver quality
deltoid	UBERON:0001476	83.32	silver quality
myocardium	UBERON:0002349	82.99	silver quality
vastus lateralis	UBERON:0001379	81.34	silver quality
quadriceps femoris	UBERON:0001377	81.04	silver quality
pigmented layer of retina	UBERON:0001782	80.80	gold quality
mucosa of sigmoid colon	UBERON:0004993	79.87	gold quality
parietal pleura	UBERON:0002400	79.74	gold quality
colonic mucosa	UBERON:0000317	79.73	gold quality
jejunum	UBERON:0002115	79.17	gold quality
jejunal mucosa	UBERON:0000399	78.89	gold quality
gastrocnemius	UBERON:0001388	78.76	gold quality
gingival epithelium	UBERON:0001949	78.49	gold quality
muscle of leg	UBERON:0001383	78.43	gold quality
pancreatic ductal cell	CL:0002079	78.38	silver quality
upper arm skin	UBERON:0004263	78.34	gold quality
muscle tissue	UBERON:0002385	78.11	gold quality
ventricular zone	UBERON:0003053	78.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.28

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2490.1	ZFP3	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605530

miRNA regulators (miRDB)

140 targeting ZFP3, 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-4533	100.00	69.48	2758
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-448	99.79	72.37	2103

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp3	ENSMUSG00000043602
rattus_norvegicus	Zfp3	ENSRNOG00000005009

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 3 homolog — Q96NJ6 (reviewed: Q96NJ6)

Alternative names: Zinc finger protein 752

All UniProt accessions (1): Q96NJ6

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 (1): NP_694563* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050888	ZnF_C2H2-type_TF	Family

Pfam: PF00096

UniProt features (20 total): zinc finger region 13, region of interest 2, compositionally biased region 2, cross-link 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96NJ6-F1	75.03	0.53

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): 6, 11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 77 (showing top): ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, ELK1_01, MARSON_BOUND_BY_FOXP3_STIMULATED, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, FIGUEROA_AML_METHYLATION_CLUSTER_1_UP, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, FIGUEROA_AML_METHYLATION_CLUSTER_4_UP, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, LIM_MAMMARY_STEM_CELL_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, SNIP1_TARGET_GENES, MIR186_5P

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (7): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

290 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZFP3	RCVRN	P35243	663
ZFP3	PTGER1	P34995	596
ZFP3	POLR2L	P52436	541
ZFP3	SPARC	P09486	521
ZFP3	TP53	P04637	519
ZFP3	SLC46A2	Q9BY10	503
ZFP3	CRABP2	P29373	446
ZFP3	RBM6	P78332	432
ZFP3	RBM27	Q9P2N5	380
ZFP3	XKR5	Q6UX68	370
ZFP3	RNF113B	Q8IZP6	367
ZFP3	UBP1	Q9NZI7	331
ZFP3	K7EJK4	K7EJK4	321
ZFP3	N4BP3	O15049	316
ZFP3	ANKRD13D	Q6ZTN6	315

IntAct

8 interactions, top by confidence:

A	B	Type	Score
YJU2B	ZFP3	psi-mi:“MI:0915”(physical association)	0.560
ZFP3	ECE1	psi-mi:“MI:0915”(physical association)	0.370
KDR	SMARCA5	psi-mi:“MI:2364”(proximity)	0.270
ZFP3	YJU2B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): ZFP3 (Two-hybrid), ZFP3 (Proximity Label-MS), ZFP3 (Proximity Label-MS), ANXA6 (Cross-Linking-MS (XL-MS)), ZFP3 (Affinity Capture-MS), ZFP3 (Affinity Capture-MS)

ESM2 similar proteins: A0JNB1, A6QLU5, O75123, O75820, P10076, P10755, P16374, P17031, P17097, P17141, P51814, Q02975, Q08ER8, Q14588, Q14590, Q32KN0, Q3V080, Q4V8A8, Q5CZA5, Q5R4K8, Q5R5Q6, Q5R9S5, Q5RBX0, Q61751, Q6GQR8, Q6P560, Q6ZMS4, Q7TSH9, Q7TSI0, Q7Z3I7, Q7Z3V5, Q8BLB0, Q8N141, Q8N184, Q8N823, Q8N8J6, Q8N9F8, Q8TBZ5, Q8TF47, Q96ND8

Diamond homologs: A1YF12, A1YG88, A2T759, P17020, Q96NJ6, Q1LZ87, Q8NF99, P18715, P18720, P18724, P18729, P18730, P18735, P18737, P18738, P18741, P18743, Q8BLB0, P08045, P18726, P18731, P18736, P18753, P18853, P51815, Q3MJ62, Q3TDE8, Q3US17, Q62513, Q62981, Q6A085, Q6NX45, Q6P1L6, Q7TNU6, Q92670, Q9UEG4, P17023, P17026, P18722, P21506

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

378 predictions. Top by Δscore:

Variant	Effect	Δscore
17:5078540:GCGGA:G	donor_gain	0.9900
17:5078545:G:GG	donor_gain	0.9900
17:5078573:GCG:G	donor_gain	0.9900
17:5078572:TGCG:T	donor_loss	0.9800
17:5078574:CG:C	donor_loss	0.9800
17:5078575:GGTGA:G	donor_loss	0.9800
17:5078576:G:GG	donor_gain	0.9800
17:5078576:GTGAG:G	donor_loss	0.9800
17:5078577:T:TC	donor_loss	0.9800
17:5078578:GA:G	donor_loss	0.9800
17:5078542:GGA:G	donor_gain	0.9600
17:5078543:GA:G	donor_gain	0.9600
17:5078543:GAG:G	donor_gain	0.9600
17:5078560:G:T	donor_gain	0.9300
17:5078579:AGA:A	donor_loss	0.9300
17:5091496:GATT:G	acceptor_gain	0.9200
17:5078542:G:GT	donor_gain	0.9100
17:5091490:ATTTC:A	acceptor_loss	0.9100
17:5091491:TTTCA:T	acceptor_loss	0.9100
17:5091492:TTCA:T	acceptor_loss	0.9100
17:5091493:TCAG:T	acceptor_loss	0.9100
17:5091494:CA:C	acceptor_loss	0.9100
17:5091495:AGA:A	acceptor_loss	0.9100
17:5091496:G:T	acceptor_loss	0.9100
17:5078499:C:G	donor_gain	0.8900
17:5091495:A:AG	acceptor_gain	0.8600
17:5091496:G:GG	acceptor_gain	0.8600
17:5078560:G:GT	donor_gain	0.8500
17:5078580:G:C	donor_loss	0.8500
17:5091701:A:T	donor_gain	0.8400

AlphaMissense

3367 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:5092120:T:C	F206L	0.999
17:5092122:C:A	F206L	0.999
17:5092122:C:G	F206L	0.999
17:5092139:T:C	L212P	0.999
17:5092204:T:C	F234L	0.999
17:5092206:C:A	F234L	0.999
17:5092206:C:G	F234L	0.999
17:5092456:T:C	F318L	0.999
17:5092458:C:A	F318L	0.999
17:5092458:C:G	F318L	0.999
17:5091952:T:C	F150L	0.998
17:5091954:T:A	F150L	0.998
17:5091954:T:G	F150L	0.998
17:5092036:T:C	F178L	0.998
17:5092038:T:A	F178L	0.998
17:5092038:T:G	F178L	0.998
17:5092061:G:C	R186P	0.998
17:5092288:T:C	F262L	0.998
17:5092290:T:A	F262L	0.998
17:5092290:T:G	F262L	0.998
17:5092307:T:C	L268P	0.998
17:5092624:T:C	F374L	0.998
17:5092626:C:A	F374L	0.998
17:5092626:C:G	F374L	0.998
17:5092708:T:C	F402L	0.998
17:5092710:C:A	F402L	0.998
17:5092710:C:G	F402L	0.998
17:5092715:G:C	R404P	0.998
17:5092876:T:C	F458L	0.998
17:5092878:T:A	F458L	0.998

dbSNP variants (sampled 300 via entrez): RS1000217058 (17:5079633 T>C), RS1000272444 (17:5086648 T>C), RS1000726620 (17:5079267 A>G), RS1000747607 (17:5091669 G>A,T), RS1000952812 (17:5091295 T>G), RS1001008682 (17:5085242 C>T), RS1001068710 (17:5091068 A>C,G), RS1001576910 (17:5086518 C>T), RS1001728468 (17:5080858 T>C), RS1001737414 (17:5078808 C>G,T), RS1001759758 (17:5080515 C>T), RS1002007935 (17:5086241 T>A), RS1002122026 (17:5077483 G>A), RS1002495878 (17:5089716 C>G,T), RS1002609278 (17:5087705 C>T)

Disease associations

OMIM: gene MIM:194480 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004744_24	Lung adenocarcinoma	5.000000e-06
GCST007540_10	PEG-asparaginase hypersensitivity without enzyme activity in childhood acute lymphoblastic leukaemia	5.000000e-06
GCST90013442_27	Keratoconus	2.000000e-14

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004881	asparaginase hypersensitivity

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066430 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.52	Kd	3008	nM	CHEMBL5653589
5.52	ED50	3008	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149810: Binding affinity to human ZFP3 incubated for 45 mins by Kinobead based pull down assay	kd	3.0078	uM

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	4
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
manganese chloride	decreases expression, increases abundance	1
beta-methylcholine	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Doxorubicin	decreases expression	1
Manganese	decreases expression, increases abundance	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Cadmium Chloride	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652852	Binding	Binding affinity to human ZFP3 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_HD05	HEK293 eGFP-ZFP3	Transformed cell line	Female

Clinical trials (associated diseases)

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