ZNF333

Summary

ZNF333 (zinc finger protein 333, HGNC:15624) is a protein-coding gene on chromosome 19p13.12, encoding Zinc finger protein 333 (Q96JL9). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-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 84449 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 113 total
• MANE Select transcript: NM_032433

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15624
Approved symbol	ZNF333
Name	zinc finger protein 333
Location	19p13.12
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1806
Ensembl gene	ENSG00000160961
Ensembl biotype	protein_coding
OMIM	611811
Entrez	84449

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 6 protein_coding, 4 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000292530, ENST00000392987, ENST00000540689, ENST00000594592, ENST00000596285, ENST00000597007, ENST00000597301, ENST00000598161, ENST00000601134, ENST00000601629, ENST00000875306, ENST00000927138, ENST00000959998

RefSeq mRNA: 7 — MANE Select: NM_032433 NM_001300912, NM_001352239, NM_001352240, NM_001352241, NM_001352243, NM_001352244, NM_032433

CCDS: CCDS12316, CCDS74298

Canonical transcript exons

ENST00000292530 — 12 exons

Exon	Start	End
ENSE00001138613	14718228	14721899
ENSE00002257902	14690048	14690150
ENSE00003459442	14699199	14699281
ENSE00003479980	14706686	14706773
ENSE00003500577	14715382	14715470
ENSE00003540154	14716994	14717089
ENSE00003581629	14695010	14695133
ENSE00003588495	14717657	14717733
ENSE00003592520	14716112	14716238
ENSE00003627673	14695566	14695661
ENSE00003658917	14705054	14705170
ENSE00003688996	14693451	14693494

Expression profiles

Bgee: expression breadth ubiquitous, 184 present calls, max score 90.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.9601 / max 68.7528, expressed in 1738 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174284	5.9601	1738

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	90.82	gold quality
mucosa of stomach	UBERON:0001199	90.31	gold quality
body of uterus	UBERON:0009853	90.22	gold quality
left ovary	UBERON:0002119	90.00	gold quality
right ovary	UBERON:0002118	89.56	gold quality
endocervix	UBERON:0000458	89.42	gold quality
left uterine tube	UBERON:0001303	88.69	gold quality
right hemisphere of cerebellum	UBERON:0014890	88.40	gold quality
cerebellar hemisphere	UBERON:0002245	88.00	gold quality
cerebellar cortex	UBERON:0002129	87.79	gold quality
monocyte	CL:0000576	87.58	gold quality
leukocyte	CL:0000738	87.20	gold quality
tibial artery	UBERON:0007610	87.17	gold quality
popliteal artery	UBERON:0002250	87.16	gold quality
tibial nerve	UBERON:0001323	87.12	gold quality
smooth muscle tissue	UBERON:0001135	87.01	gold quality
muscle layer of sigmoid colon	UBERON:0035805	86.84	gold quality
ectocervix	UBERON:0012249	86.70	gold quality
aorta	UBERON:0000947	86.66	gold quality
ascending aorta	UBERON:0001496	86.38	gold quality
thoracic aorta	UBERON:0001515	86.38	gold quality
descending thoracic aorta	UBERON:0002345	86.33	gold quality
granulocyte	CL:0000094	86.09	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.91	gold quality
right uterine tube	UBERON:0001302	85.87	gold quality
cerebellum	UBERON:0002037	85.83	gold quality
lower esophagus muscularis layer	UBERON:0035833	85.66	gold quality
lower esophagus	UBERON:0013473	85.60	gold quality
ovary	UBERON:0000992	85.33	gold quality
left coronary artery	UBERON:0001626	84.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.59
E-CURD-97	no	171.74

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

94 targeting ZNF333, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514

Literature-anchored findings (GeneRIF, showing 2)

• dna sequence analysis of ZNF333 gene located on chromosome 19p13.1 (PMID:12151103)
• ZNF333 recognized the specific DNA core binding sequence ATAAT (PMID:15607024)

Cross-species orthologs

0 orthologs

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

Zinc finger protein 333 — Q96JL9 (reviewed: Q96JL9)

All UniProt accessions (4): Q96JL9, M0R0S8, M0R113, M0R1P1

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in heart.

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

Isoforms (3)

UniProt ID	Names	Canonical?
Q96JL9-1	1	yes
Q96JL9-2	2
Q96JL9-3	3

RefSeq proteins (7): NP_001287841, NP_001339168, NP_001339169, NP_001339170, NP_001339172, NP_001339173, NP_115809* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352, PF13465

UniProt features (20 total): zinc finger region 10, splice variant 4, domain 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96JL9-F1	58.76	0.13

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 59 (showing top): MODULE_48, MODULE_95, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, PEDRIOLI_MIR31_TARGETS_DN, MODULE_163, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GSE14415_NATURAL_TREG_VS_TCONV_UP, ELF2_TARGET_GENES, ZNF407_TARGET_GENES, MIR4795_3P, MIR4729, MIR548AR_3P, MIR4728_5P, MIR4753_3P

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), 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)

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
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	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
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

544 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF333	ING4	Q9UNL4	567
ZNF333	TMEM161B	Q8NDZ6	397
ZNF333	ARHGAP36	Q6ZRI8	387
ZNF333	MEF2A	Q02078	386
ZNF333	NFIA	Q12857	377
ZNF333	HARS1	P12081	374
ZNF333	SON	P18583	371
ZNF333	PPP1CC	P36873	352
ZNF333	PABIR2	Q7Z309	351
ZNF333	GPC4	O75487	348
ZNF333	DDX1	Q92499	332
ZNF333	G3V325	G3V325	324
ZNF333	TTC13	Q8NBP0	321
ZNF333	AKNAD1	Q5T1N1	310
ZNF333	ZNF474	Q6S9Z5	305
ZNF333	SLFN12	Q8IYM2	305

IntAct

8 interactions, top by confidence:

A	B	Type	Score
ZNF333	TRIM28	psi-mi:“MI:0915”(physical association)	0.620
KDM1A	ZNF333	psi-mi:“MI:0915”(physical association)	0.370
ZNF333	ZDHHC17	psi-mi:“MI:0915”(physical association)	0.370
ZNF333	ASPM	psi-mi:“MI:0914”(association)	0.350
ZNF333	TRIM24	psi-mi:“MI:0914”(association)	0.350
ZNF333	ZNF195	psi-mi:“MI:0914”(association)	0.350

BioGRID (25): ZNF333 (Two-hybrid), TRIM28 (Affinity Capture-MS), TYK2 (Affinity Capture-MS), ARL15 (Affinity Capture-MS), ASPM (Affinity Capture-MS), ZNF333 (Two-hybrid), ZNF333 (Affinity Capture-MS), ZNF333 (Affinity Capture-MS), ZNF333 (Two-hybrid), ZNF333 (Two-hybrid), TRIM28 (Affinity Capture-MS), HJURP (Affinity Capture-MS), SENP5 (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), MTPAP (Affinity Capture-MS)

ESM2 similar proteins: A1A5P9, A2AVR2, A6QPT6, B2KFW1, O14978, P17029, P17040, P17098, P25233, P70503, Q13342, Q14D33, Q3SYK4, Q3V3Q4, Q4KLI1, Q4R8H9, Q4V8E9, Q5PPP4, Q5R670, Q5R7U0, Q5VWK0, Q61066, Q63HK3, Q68CQ1, Q6PCZ4, Q7TS72, Q80ZG2, Q8BGS3, Q8CF60, Q8IWY8, Q8N660, Q8NDZ0, Q8TD17, Q921B4, Q923B3, Q96D09, Q96GC6, Q96JL9, Q96M43, Q99608

Diamond homologs: A0A1W2PQL4, A0JNB1, A0JPL0, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MT65, A8MUV8, A8MWA4, B2RXC5, B4DU55, B4DX44, E9PYI1, O14628, O75346, P0CH99, P0CI00, P17014, P17030, P17032, P17098, P51786, P85977, Q02386, Q06730, Q06732, Q0VAW7, Q12901, Q13360, Q14586, Q14588, Q14590, Q16587, Q2M3X9, Q2VY69, Q32M78, Q3ZCX4, Q49AA0, Q4R6J4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	93
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2469 predictions. Top by Δscore:

Variant	Effect	Δscore
19:14695099:G:GT	donor_gain	1.0000
19:14695131:GGG:G	donor_gain	1.0000
19:14695132:GGG:G	donor_gain	1.0000
19:14695558:AT:A	acceptor_gain	1.0000
19:14695559:T:G	acceptor_gain	1.0000
19:14695564:A:AC	acceptor_loss	1.0000
19:14695564:A:AG	acceptor_gain	1.0000
19:14695564:AG:A	acceptor_gain	1.0000
19:14695565:G:GT	acceptor_gain	1.0000
19:14695565:GG:G	acceptor_gain	1.0000
19:14695565:GGA:G	acceptor_gain	1.0000
19:14695565:GGAA:G	acceptor_gain	1.0000
19:14695658:GTTG:G	donor_gain	1.0000
19:14695662:G:GC	donor_loss	1.0000
19:14695662:G:GG	donor_gain	1.0000
19:14695663:TGAG:T	donor_loss	1.0000
19:14695665:AGT:A	donor_loss	1.0000
19:14699197:A:AG	acceptor_gain	1.0000
19:14699197:AGCCT:A	acceptor_gain	1.0000
19:14699198:G:GC	acceptor_gain	1.0000
19:14699198:GCCT:G	acceptor_gain	1.0000
19:14699198:GCCTG:G	acceptor_gain	1.0000
19:14699278:AATGG:A	donor_loss	1.0000
19:14699280:TGG:T	donor_loss	1.0000
19:14699282:GTA:G	donor_loss	1.0000
19:14699283:T:A	donor_loss	1.0000
19:14705167:CACG:C	donor_loss	1.0000
19:14705168:ACG:A	donor_loss	1.0000
19:14705169:CGG:C	donor_loss	1.0000
19:14705171:GT:G	donor_loss	1.0000

AlphaMissense

4382 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:14718702:T:C	F459L	0.999
19:14718704:C:A	F459L	0.999
19:14718704:C:G	F459L	0.999
19:14719038:T:C	F571L	0.999
19:14719040:C:A	F571L	0.999
19:14719040:C:G	F571L	0.999
19:14719122:T:C	F599L	0.999
19:14719124:T:A	F599L	0.999
19:14719124:T:G	F599L	0.999
19:14718786:T:C	F487L	0.998
19:14718788:C:A	F487L	0.998
19:14718788:C:G	F487L	0.998
19:14719206:T:C	F627L	0.998
19:14719208:C:A	F627L	0.998
19:14719208:C:G	F627L	0.998
19:14718618:T:C	F431L	0.997
19:14718620:C:A	F431L	0.997
19:14718620:C:G	F431L	0.997
19:14718637:T:C	L437P	0.997
19:14718659:C:A	H444Q	0.997
19:14718659:C:G	H444Q	0.997
19:14718731:C:A	H468Q	0.997
19:14718731:C:G	H468Q	0.997
19:14718870:T:C	F515L	0.997
19:14718872:C:A	F515L	0.997
19:14718872:C:G	F515L	0.997
19:14716146:T:C	F212S	0.996
19:14718534:T:C	F403L	0.996
19:14718536:C:A	F403L	0.996
19:14718536:C:G	F403L	0.996

dbSNP variants (sampled 300 via entrez): RS1000129148 (19:14706870 ACTGCAGGCACTGCCGTGG>A), RS1000297069 (19:14714250 G>A), RS1000373204 (19:14708306 C>T), RS1000446831 (19:14690041 A>G), RS1000560575 (19:14690233 T>A), RS1000608711 (19:14729372 G>GT), RS1000693450 (19:14717786 G>A,C,T), RS1000766168 (19:14702851 C>T), RS1000783823 (19:14720932 A>G), RS1000785217 (19:14720540 A>G), RS1000798363 (19:14724794 G>A,T), RS1000811382 (19:14689801 A>C), RS1000880915 (19:14697820 A>T), RS1000919780 (19:14702012 C>G), RS1000951503 (19:14696406 A>G)

Disease associations

OMIM: gene MIM:611811 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST007059_3	Response to antidepressants (symptom improvement)	5.000000e-06
GCST90002401_255	Platelet distribution width	2.000000e-19

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
NSC 689534	increases expression, affects binding	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Copper	affects binding, increases expression	1
Doxorubicin	decreases expression	1
Methotrexate	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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