ZNF84

Summary

ZNF84 (zinc finger protein 84, HGNC:13159) is a protein-coding gene on chromosome 12q24.33, encoding Zinc finger protein 84 (P51523). May be involved in transcriptional regulation.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 7637 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 23 total
• MANE Select transcript: NM_001289971

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13159
Approved symbol	ZNF84
Name	zinc finger protein 84
Location	12q24.33
Locus type	gene with protein product
Status	Approved
Aliases	HPF2
Ensembl gene	ENSG00000198040
Ensembl biotype	protein_coding
OMIM	618554
Entrez	7637

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 30 protein_coding, 5 retained_intron

ENST00000327668, ENST00000392319, ENST00000438628, ENST00000441040, ENST00000535439, ENST00000536123, ENST00000539098, ENST00000539354, ENST00000539686, ENST00000540031, ENST00000542358, ENST00000542874, ENST00000543124, ENST00000543310, ENST00000543758, ENST00000545299, ENST00000907399, ENST00000907400, ENST00000907401, ENST00000907402, ENST00000907403, ENST00000907404, ENST00000907405, ENST00000907406, ENST00000917405, ENST00000917406, ENST00000917407, ENST00000917408, ENST00000917409, ENST00000917410, ENST00000960324, ENST00000960325, ENST00000960326, ENST00000960327, ENST00000960328

RefSeq mRNA: 4 — MANE Select: NM_001289971 NM_001127372, NM_001289971, NM_001289972, NM_003428

CCDS: CCDS31940

Canonical transcript exons

ENST00000539354 — 5 exons

Exon	Start	End
ENSE00002276382	133056954	133063299
ENSE00002313279	133037509	133037545
ENSE00003572129	133047955	133048081
ENSE00003591720	133048753	133048848
ENSE00003605131	133041278	133041482

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 95.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.8539 / max 105.7119, expressed in 1735 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128853	6.8789	1648
128852	2.1583	1048
128851	0.7040	364
128850	0.6813	381
128854	0.4315	226

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	95.93	gold quality
ganglionic eminence	UBERON:0004023	94.63	gold quality
calcaneal tendon	UBERON:0003701	92.54	gold quality
embryo	UBERON:0000922	92.52	gold quality
right uterine tube	UBERON:0001302	91.66	gold quality
ventricular zone	UBERON:0003053	91.44	gold quality
Brodmann (1909) area 23	UBERON:0013554	91.38	gold quality
oocyte	CL:0000023	90.83	gold quality
middle temporal gyrus	UBERON:0002771	90.59	gold quality
postcentral gyrus	UBERON:0002581	90.01	gold quality
corpus callosum	UBERON:0002336	89.79	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.31	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.11	gold quality
secondary oocyte	CL:0000655	89.07	gold quality
adrenal tissue	UBERON:0018303	89.00	gold quality
germinal epithelium of ovary	UBERON:0001304	88.99	gold quality
parietal lobe	UBERON:0001872	88.92	gold quality
corpus epididymis	UBERON:0004359	88.31	gold quality
entorhinal cortex	UBERON:0002728	88.16	gold quality
caput epididymis	UBERON:0004358	88.14	gold quality
superior frontal gyrus	UBERON:0002661	88.12	gold quality
sural nerve	UBERON:0015488	88.03	gold quality
pituitary gland	UBERON:0000007	87.59	gold quality
endometrium	UBERON:0001295	87.49	gold quality
ovary	UBERON:0000992	87.20	gold quality
left ovary	UBERON:0002119	87.07	gold quality
adenohypophysis	UBERON:0002196	86.73	gold quality
cauda epididymis	UBERON:0004360	86.72	gold quality
colonic epithelium	UBERON:0000397	86.53	gold quality
right ovary	UBERON:0002118	86.46	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.94

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

161 targeting ZNF84, 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-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-5696	99.98	72.36	4487
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-539-3P	99.98	70.74	1616
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-12136	99.98	72.81	5713
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-450B-5P	99.92	71.48	3175

Literature-anchored findings (GeneRIF, showing 2)

• FISH assignment to chromosome 12q24.33; gene organization and splicing (PMID:11856868)
• ZNF84 expression was increased in CC [cervical cancer ] tissues and associated with tumor size. ZNF84 promoted cell proliferation which might involve Akt signal. (PMID:29610946)

Cross-species orthologs

16 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf646	ENSDARG00000061424
danio_rerio	si:dkey-154p10.3	ENSDARG00000068366
danio_rerio	si:dkey-89b17.4	ENSDARG00000075545
danio_rerio	zgc:66472	ENSDARG00000075916
danio_rerio	si:ch211-148l7.4	ENSDARG00000094469
danio_rerio	znf576.1	ENSDARG00000097819
drosophila_melanogaster	az2	FBGN0025185
drosophila_melanogaster	CG2129	FBGN0030008
drosophila_melanogaster	CG1602	FBGN0033186
drosophila_melanogaster	CG18011	FBGN0033491
drosophila_melanogaster	CG12942	FBGN0033569
drosophila_melanogaster	indra	FBGN0035213
drosophila_melanogaster	CG30020	FBGN0050020
drosophila_melanogaster	mld	FBGN0263490
caenorhabditis_elegans	ztf-15	WBGENE00011066
caenorhabditis_elegans		WBGENE00015649

Paralogs (36): ZNF302 (ENSG00000089335), ZNF184 (ENSG00000096654), CTCF (ENSG00000102974), ZNF574 (ENSG00000105732), ZBTB24 (ENSG00000112365), ZNF142 (ENSG00000115568), CTCFL (ENSG00000124092), ZNF473 (ENSG00000142528), ZNF827 (ENSG00000151612), ZNF689 (ENSG00000156853), ZNF208 (ENSG00000160321), ZNF91 (ENSG00000167232), ZNF526 (ENSG00000167625), ZNF764 (ENSG00000169951), ZNF747 (ENSG00000169955), ZNF282 (ENSG00000170265), ZNF160 (ENSG00000170949), ZNF497 (ENSG00000174586), ZBTB34 (ENSG00000177125), ZNF771 (ENSG00000179965), ZNF48 (ENSG00000180035), ZNF594 (ENSG00000180626), ZBTB37 (ENSG00000185278), ZFP92 (ENSG00000189420), ZNF107 (ENSG00000196247), ZNF729 (ENSG00000196350), ZNF569 (ENSG00000196437), ZNF420 (ENSG00000197050), ZNF785 (ENSG00000197162), ZNF665 (ENSG00000197497), ZNF181 (ENSG00000197841), ZNF347 (ENSG00000197937), ZBTB48 (ENSG00000204859), ZNF845 (ENSG00000213799), ZNF99 (ENSG00000213973), ZNF688 (ENSG00000229809)

Protein

Protein identifiers

Zinc finger protein 84 — P51523 (reviewed: P51523)

Alternative names: Zinc finger protein HPF2

All UniProt accessions (8): P51523, F5H0T0, F5H1B1, F5H1R3, F5H3F5, F5H630, F5H6X5, J3KQ53

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 (4): NP_001120844, NP_001276900, NP_001276901, NP_003419 (=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

Pfam: PF00096, PF01352

UniProt features (28 total): zinc finger region 19, cross-link 4, sequence conflict 2, chain 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P51523-F1	75.61	0.35

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 (5): 128, 112, 125, 191, 457

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 110 (showing top): WU_APOPTOSIS_BY_CDKN1A_VIA_TP53, GCM_MAP4K4, GCM_GSPT1, ONKEN_UVEAL_MELANOMA_UP, GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, GCM_SUFU, DODD_NASOPHARYNGEAL_CARCINOMA_UP, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, GCM_NF2, GCM_CALM1, WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT, GCM_MAP1B, GCM_RBM8A, GRADE_COLON_AND_RECTAL_CANCER_UP

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), regulation of macromolecule metabolic process (GO:0060255), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (4): DNA binding (GO:0003677), 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
regulation of metabolic process	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
macromolecule metabolic process	1
primary metabolic process	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

582 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF84	ZNF280A	P59817	504
ZNF84	PARP2	Q9UGN5	494
ZNF84	TRIM28	Q13263	490
ZNF84	ZNF200	P98182	462
ZNF84	ZNF382	Q96SR6	455
ZNF84	ZNF668	Q96K58	447
ZNF84	KIAA0408	Q6ZU52	442
ZNF84	ZNF511	Q8NB15	370
ZNF84	OLIG3	Q7RTU3	368
ZNF84	SEPHS1	P49903	359
ZNF84	SPRY1	O43609	353
ZNF84	NFIC	P08651	353
ZNF84	SLC6A1	P30531	353
ZNF84	PDGFC	Q9NRA1	353
ZNF84	TCF12	Q99081	348

IntAct

27 interactions, top by confidence:

A	B	Type	Score
HSF2BP	ZNF84	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	ZNF84	psi-mi:“MI:0915”(physical association)	0.560
LMO1	ZNF84	psi-mi:“MI:0915”(physical association)	0.560
ZNF84	SPANXN2	psi-mi:“MI:0915”(physical association)	0.560
ZNF84	LMO3	psi-mi:“MI:0915”(physical association)	0.560
ZNF84	TRIM28	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF84	E2	psi-mi:“MI:0915”(physical association)	0.490
ZNF84	NOP2	psi-mi:“MI:0915”(physical association)	0.400
ZNF84	ECE1	psi-mi:“MI:0915”(physical association)	0.370
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF84	E2	psi-mi:“MI:0915”(physical association)	0.000
LMO3	ZNF84	psi-mi:“MI:0915”(physical association)	0.000
ZNF84		psi-mi:“MI:0915”(physical association)	0.000
WDR4	ZNF84	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (15): ZNF84 (Reconstituted Complex), ZNF84 (Affinity Capture-MS), ZNF84 (Affinity Capture-RNA), ZNF84 (Two-hybrid), ZNF84 (Two-hybrid), ZNF84 (Two-hybrid), SPANXN2 (Two-hybrid), ZNF84 (Proximity Label-MS), ZNF84 (Affinity Capture-MS), ZNF84 (Affinity Capture-MS), ZNF84 (Affinity Capture-MS), ZNF84 (Two-hybrid), NUP85 (Cross-Linking-MS (XL-MS)), ZNF84 (Affinity Capture-MS), ZNF84 (Two-hybrid)

ESM2 similar proteins: A2VDQ7, A6NNF4, A8MQ14, A8MTY0, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17027, P17039, P35789, P51522, P51523, Q08AN1, Q14585, Q14587, Q3SYV7, Q3ZCX4, Q4R4C7, Q52M93, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6ECI4, Q6JLC9, Q6P3V2, Q6P5C7, Q6ZN57, Q86UE3, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N7M2

Diamond homologs: A0JPL0, A2VDP4, A6QLU5, A6QPT6, A8MQ14, A8MUZ8, A8MWA4, B1APH4, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, P08042, P0CH99, P0CI00, P17014, P17025, P17030, P17031, P17032, P17098, P21506, P51508, P51523, P51786, P51814, P52736, P52738, Q02525, Q03923, Q03936, Q06730, Q06732, Q0VCB0, Q13401, Q14587, Q16587, Q2M218, Q2M3X9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1217 predictions. Top by Δscore:

Variant	Effect	Δscore
12:133037550:GTTCA:G	donor_gain	1.0000
12:133037546:G:GG	donor_gain	0.9900
12:133037551:T:G	donor_gain	0.9900
12:133037555:G:GG	donor_gain	0.9900
12:133048042:G:GT	donor_gain	0.9900
12:133048845:CCAGG:C	donor_loss	0.9900
12:133048848:GGT:G	donor_loss	0.9900
12:133048849:G:T	donor_loss	0.9900
12:133048850:T:TC	donor_loss	0.9900
12:133037355:G:T	donor_gain	0.9800
12:133048751:AG:A	acceptor_gain	0.9800
12:133048752:GG:G	acceptor_gain	0.9800
12:133048851:G:GT	donor_loss	0.9800
12:133048748:AACAG:A	acceptor_gain	0.9700
12:133048751:A:AG	acceptor_gain	0.9700
12:133048752:G:GG	acceptor_gain	0.9700
12:133037544:TTG:T	donor_loss	0.9600
12:133037545:TG:T	donor_loss	0.9600
12:133037546:GTGA:G	donor_loss	0.9600
12:133041479:ACAG:A	donor_loss	0.9600
12:133041480:CAGGT:C	donor_loss	0.9600
12:133041481:AGG:A	donor_loss	0.9600
12:133041482:GGT:G	donor_loss	0.9600
12:133041483:G:GA	donor_loss	0.9600
12:133041484:T:G	donor_loss	0.9600
12:133037542:TTTT:T	donor_gain	0.9500
12:133037544:TT:T	donor_gain	0.9500
12:133037547:T:A	donor_loss	0.9500
12:133037549:AG:A	donor_loss	0.9500
12:133038010:A:AG	donor_gain	0.9500

AlphaMissense

4951 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:133057529:T:C	F272L	0.999
12:133057531:C:A	F272L	0.999
12:133057531:C:G	F272L	0.999
12:133057548:T:C	L278P	0.999
12:133057563:G:C	R283P	0.999
12:133057613:T:C	F300L	0.999
12:133057615:C:A	F300L	0.999
12:133057615:C:G	F300L	0.999
12:133057620:G:C	R302P	0.999
12:133057632:T:C	L306P	0.999
12:133057697:T:C	F328L	0.999
12:133057699:T:A	F328L	0.999
12:133057699:T:G	F328L	0.999
12:133057716:T:C	L334P	0.999
12:133057781:T:C	F356L	0.999
12:133057783:C:A	F356L	0.999
12:133057783:C:G	F356L	0.999
12:133057949:T:C	F412L	0.999
12:133057951:T:A	F412L	0.999
12:133057951:T:G	F412L	0.999
12:133058033:T:C	F440L	0.999
12:133058035:C:A	F440L	0.999
12:133058035:C:G	F440L	0.999
12:133058052:T:C	L446P	0.999
12:133058117:T:C	F468L	0.999
12:133058119:C:A	F468L	0.999
12:133058119:C:G	F468L	0.999
12:133058285:T:C	F524L	0.999
12:133058287:T:A	F524L	0.999
12:133058287:T:G	F524L	0.999

dbSNP variants (sampled 300 via entrez): RS1000003753 (12:133056299 G>A,C), RS1000338308 (12:133062934 A>G), RS1000515326 (12:133050876 A>C), RS1000687647 (12:133044838 T>C), RS1000737825 (12:133044698 G>A,C,T), RS1000753952 (12:133038753 C>T), RS1000887873 (12:133063602 C>T), RS1000955828 (12:133058100 G>C), RS1000971017 (12:133050515 T>A), RS1001207692 (12:133038462 G>A), RS1001327210 (12:133062060 A>C,G), RS1001441480 (12:133062354 T>C), RS1001541127 (12:133038389 T>C), RS1001581898 (12:133044323 T>G), RS1001593562 (12:133038137 C>T)

Disease associations

OMIM: gene MIM:618554 | 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
Valproic Acid	decreases methylation, affects expression, decreases expression	5
sodium arsenite	decreases expression	3
entinostat	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
Aflatoxin B1	affects expression, increases methylation	2
aristolochic acid I	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
geraniol	increases expression	1
manganese chloride	increases abundance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Coumestrol	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Gallic Acid	decreases expression	1
Manganese	increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1

Clinical trials (associated diseases)

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