ZNF484

Summary

ZNF484 (zinc finger protein 484, HGNC:23385) is a protein-coding gene on chromosome 9q22.31, encoding Zinc finger protein 484 (Q5JVG2). May be involved in transcriptional regulation.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 83744 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 118 total
• MANE Select transcript: NM_031486

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23385
Approved symbol	ZNF484
Name	zinc finger protein 484
Location	9q22.31
Locus type	gene with protein product
Status	Approved
Aliases	BA526D8.4, FLJ33884
Ensembl gene	ENSG00000127081
Ensembl biotype	protein_coding
Entrez	83744

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000332591, ENST00000375495, ENST00000395505, ENST00000395506, ENST00000718324, ENST00000855340, ENST00000855341, ENST00000855342

RefSeq mRNA: 7 — MANE Select: NM_031486 NM_001007101, NM_001261458, NM_001261459, NM_001261460, NM_001354536, NM_001354537, NM_031486

CCDS: CCDS35066, CCDS35067, CCDS59136

Canonical transcript exons

ENST00000375495 — 5 exons

Exon	Start	End
ENSE00000869903	92855811	92855903
ENSE00002258811	92875015	92875059
ENSE00003685220	92856192	92856318
ENSE00004034781	92877890	92878038
ENSE00004034782	92844182	92848551

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 87.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.8996 / max 215.3042, expressed in 1519 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
101453	5.8996	1519

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	87.67	gold quality
calcaneal tendon	UBERON:0003701	84.04	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.50	gold quality
adrenal tissue	UBERON:0018303	79.51	gold quality
ganglionic eminence	UBERON:0004023	78.97	gold quality
cortical plate	UBERON:0005343	78.47	gold quality
ventricular zone	UBERON:0003053	77.52	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.05	gold quality
colonic epithelium	UBERON:0000397	75.54	gold quality
islet of Langerhans	UBERON:0000006	74.78	gold quality
bone marrow cell	CL:0002092	73.56	silver quality
bone marrow	UBERON:0002371	73.48	gold quality
stromal cell of endometrium	CL:0002255	73.33	gold quality
tonsil	UBERON:0002372	73.10	gold quality
endometrium	UBERON:0001295	72.43	gold quality
superior frontal gyrus	UBERON:0002661	72.04	gold quality
cerebellar cortex	UBERON:0002129	71.71	gold quality
cerebellum	UBERON:0002037	71.70	gold quality
cerebellar hemisphere	UBERON:0002245	71.56	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.26	gold quality
sural nerve	UBERON:0015488	71.02	gold quality
leukocyte	CL:0000738	70.78	gold quality
smooth muscle tissue	UBERON:0001135	70.77	gold quality
monocyte	CL:0000576	70.59	gold quality
prefrontal cortex	UBERON:0000451	70.30	gold quality
primary visual cortex	UBERON:0002436	70.20	gold quality
lymph node	UBERON:0000029	69.63	gold quality
urinary bladder	UBERON:0001255	69.32	gold quality
frontal cortex	UBERON:0001870	68.91	gold quality
placenta	UBERON:0001987	68.90	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting ZNF484, 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-3924	100.00	72.09	2394
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4495	99.82	72.08	3080
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
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-548A-3P	99.76	70.58	3524

Cross-species orthologs

0 orthologs

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), 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), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 484 — Q5JVG2 (reviewed: Q5JVG2)

All UniProt accessions (1): Q5JVG2

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.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5JVG2-1	1	yes
Q5JVG2-2	2
Q5JVG2-3	3

RefSeq proteins (7): NP_001007102, NP_001248387, NP_001248388, NP_001248389, NP_001341465, NP_001341466, NP_113674* (*=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 (77 total): strand 29, zinc finger region 19, helix 17, turn 5, cross-link 2, splice variant 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

13 structures.

PDB	Method	Resolution (Å)
2EMF	SOLUTION NMR
2EMG	SOLUTION NMR
2EMH	SOLUTION NMR
2EMI	SOLUTION NMR
2EOV	SOLUTION NMR
2EP1	SOLUTION NMR
2EP2	SOLUTION NMR
2EP3	SOLUTION NMR
2EQW	SOLUTION NMR
2YTJ	SOLUTION NMR
2YTO	SOLUTION NMR
2YTP	SOLUTION NMR
2YTS	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JVG2-F1	60.52	0.11

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): 156, 816

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 74 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, chr9q22, CUI_TCF21_TARGETS_2_DN, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, LEE_BMP2_TARGETS_DN, PEDRIOLI_MIR31_TARGETS_UP, RAO_BOUND_BY_SALL4_ISOFORM_B, ARID5B_TARGET_GENES, ARNT2_TARGET_GENES, ATF5_TARGET_GENES, BARX1_TARGET_GENES, CIITA_TARGET_GENES, DIDO1_TARGET_GENES, E2F2_TARGET_GENES

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

GO Molecular Function (3): DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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
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
nucleic acid binding	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

312 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF484	SMIM9	A6NGZ8	638
ZNF484	SMIM19	Q96E16	514
ZNF484	MGAT4B	Q9UQ53	343
ZNF484	CSTF2T	Q9H0L4	338
ZNF484	INO80D	Q53TQ3	325
ZNF484	RNF121	Q9H920	323
ZNF484	PRRC2C	Q9Y520	316
ZNF484	GTF2IRD1	Q9UHL9	308
ZNF484	HMBOX1	Q6NT76	304
ZNF484	AAMP	Q13685	301
ZNF484	FOXN2	P32314	272
ZNF484	STK36	Q9NRP7	265
ZNF484	UQCRQ	O14949	263
ZNF484	COX7A2	P14406	254
ZNF484	PCGF5	Q86SE9	247
ZNF484	ENSA	O43768	247

IntAct

7 interactions, top by confidence:

A	B	Type	Score
ZNF484	KRT8	psi-mi:“MI:0915”(physical association)	0.400
M		psi-mi:“MI:0914”(association)	0.350
ZNF484	IPO8	psi-mi:“MI:0914”(association)	0.350
ZNF484	ZNF195	psi-mi:“MI:0914”(association)	0.350
	ZNF484	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): ZNF484 (Affinity Capture-RNA), ZNF484 (Affinity Capture-RNA), ZNF484 (Proximity Label-MS), TRIM33 (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), ZNF195 (Affinity Capture-MS), SMARCAD1 (Affinity Capture-MS), TRIM28 (Affinity Capture-MS), TRIM24 (Affinity Capture-MS), TRIM37 (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), ZYG11A (Affinity Capture-MS), ZNF484 (Protein-peptide)

ESM2 similar proteins: A2VDP4, A6NHJ4, O94892, P0CJ79, P17014, P17021, P17025, P17032, P17035, P18733, P51508, P51814, Q06730, Q06732, Q09FC8, Q0VGE8, Q14586, Q32M78, Q3MIS6, Q5JVG2, Q5R4K8, Q5R9S5, Q5RBQ3, Q5RCJ2, Q5RER9, Q5TYW1, Q5VIY5, Q6P560, Q6PDB4, Q6ZMW2, Q6ZN06, Q6ZNA1, Q76KX8, Q7L2R6, Q86Y25, Q8N184, Q8N823, Q8N883, Q8N8J6, Q8NEP9

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	102
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

997 predictions. Top by Δscore:

Variant	Effect	Δscore
9:92848547:CCCAT:C	acceptor_gain	1.0000
9:92848548:CCAT:C	acceptor_gain	1.0000
9:92848548:CCATC:C	acceptor_gain	1.0000
9:92848549:CAT:C	acceptor_gain	1.0000
9:92848549:CATC:C	acceptor_gain	1.0000
9:92848551:TCTAA:T	acceptor_loss	1.0000
9:92848552:C:CC	acceptor_gain	1.0000
9:92854094:C:CT	acceptor_gain	1.0000
9:92854095:A:T	acceptor_gain	1.0000
9:92856190:A:AC	donor_gain	1.0000
9:92856191:C:CC	donor_gain	1.0000
9:92856191:CCCA:C	donor_gain	1.0000
9:92856316:TTC:T	acceptor_gain	1.0000
9:92856317:TC:T	acceptor_gain	1.0000
9:92856318:CC:C	acceptor_gain	1.0000
9:92856319:C:CA	acceptor_loss	1.0000
9:92856319:C:CC	acceptor_gain	1.0000
9:92856320:T:A	acceptor_loss	1.0000
9:92848550:AT:A	acceptor_gain	0.9900
9:92854089:T:TC	acceptor_gain	0.9900
9:92854094:C:T	acceptor_gain	0.9900
9:92855900:CATC:C	acceptor_gain	0.9900
9:92855901:ATCCT:A	acceptor_loss	0.9900
9:92855902:TC:T	acceptor_gain	0.9900
9:92855903:CC:C	acceptor_gain	0.9900
9:92855903:CCTGT:C	acceptor_loss	0.9900
9:92855904:C:CC	acceptor_gain	0.9900
9:92855905:T:A	acceptor_loss	0.9900
9:92855911:C:CT	acceptor_gain	0.9900
9:92856186:GCTT:G	donor_loss	0.9900

AlphaMissense

5727 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:92846600:G:C	F729L	0.999
9:92846600:G:T	F729L	0.999
9:92846602:A:G	F729L	0.999
9:92846684:A:C	F701L	0.999
9:92846684:A:T	F701L	0.999
9:92846686:A:G	F701L	0.999
9:92846768:G:C	F673L	0.999
9:92846768:G:T	F673L	0.999
9:92846770:A:G	F673L	0.999
9:92846852:A:C	F645L	0.999
9:92846852:A:T	F645L	0.999
9:92846854:A:G	F645L	0.999
9:92847255:A:G	L511P	0.999
9:92846432:G:C	F785L	0.998
9:92846432:G:T	F785L	0.998
9:92846434:A:G	F785L	0.998
9:92846516:G:C	F757L	0.998
9:92846516:G:T	F757L	0.998
9:92846518:A:G	F757L	0.998
9:92846751:A:G	L679P	0.998
9:92846825:G:C	H654Q	0.998
9:92846825:G:T	H654Q	0.998
9:92846936:G:C	F617L	0.998
9:92846936:G:T	F617L	0.998
9:92846938:A:G	F617L	0.998
9:92847104:G:C	F561L	0.998
9:92847104:G:T	F561L	0.998
9:92847106:A:G	F561L	0.998
9:92847272:A:C	F505L	0.998
9:92847272:A:T	F505L	0.998

dbSNP variants (sampled 300 via entrez): RS1000092652 (9:92849798 CTCTT>C), RS1000347631 (9:92877720 C>T), RS1000446508 (9:92850095 C>T), RS1000448579 (9:92871564 A>T), RS1000643068 (9:92878977 T>C), RS1000739784 (9:92871826 C>T), RS1000756193 (9:92849859 T>C), RS1000907012 (9:92857345 G>T), RS1001078312 (9:92878752 C>T), RS1001088301 (9:92871858 G>A,T), RS1001371921 (9:92851469 G>A), RS1001633797 (9:92870887 G>A), RS1001698708 (9:92851754 T>C), RS1001705699 (9:92874098 C>A,T), RS1001777840 (9:92873824 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001524_22	Visceral adipose tissue/subcutaneous adipose tissue ratio	2.000000e-06
GCST006979_360	Heel bone mineral density	2.000000e-23
GCST010725_16	Malaria	9.000000e-06
GCST010725_28	Malaria	6.000000e-06
GCST010725_95	Malaria	6.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004767	visceral:subcutaneous adipose tissue ratio
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression	2
Particulate Matter	decreases reaction, increases expression, increases abundance	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
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
cupric oxide	increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	increases expression, decreases reaction	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Vehicle Emissions	decreases reaction, increases expression	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Urethane	increases expression	1
Vanadates	decreases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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