ZNF428

Summary

ZNF428 (zinc finger protein 428, HGNC:20804) is a protein-coding gene on chromosome 19q13.31, encoding Zinc finger protein 428 (Q96B54).

Predicted to enable zinc ion binding activity. Located in mitochondrion.

Source: NCBI Gene 126299 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_182498

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20804
Approved symbol	ZNF428
Name	zinc finger protein 428
Location	19q13.31
Locus type	gene with protein product
Status	Approved
Aliases	MGC51082, Zfp428
Ensembl gene	ENSG00000131116
Ensembl biotype	protein_coding
Entrez	126299

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 14 protein_coding, 1 retained_intron

ENST00000300811, ENST00000595304, ENST00000598676, ENST00000855578, ENST00000855579, ENST00000855580, ENST00000855581, ENST00000855582, ENST00000855583, ENST00000855584, ENST00000855585, ENST00000855586, ENST00000855587, ENST00000855588, ENST00000855589

RefSeq mRNA: 1 — MANE Select: NM_182498 NM_182498

CCDS: CCDS12626

Canonical transcript exons

ENST00000300811 — 3 exons

Exon	Start	End
ENSE00001112415	43607224	43608107
ENSE00001374602	43619558	43619629
ENSE00001404526	43614229	43614434

Expression profiles

Bgee: expression breadth ubiquitous, 219 present calls, max score 99.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 41.9262 / max 626.7953, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181295	41.4634	1822
181296	0.4628	230

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	99.07	gold quality
ganglionic eminence	UBERON:0004023	98.68	gold quality
ventricular zone	UBERON:0003053	97.64	gold quality
cingulate cortex	UBERON:0003027	96.50	gold quality
anterior cingulate cortex	UBERON:0009835	96.50	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.48	gold quality
right frontal lobe	UBERON:0002810	96.07	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	95.95	gold quality
Brodmann (1909) area 10	UBERON:0013541	95.63	gold quality
prefrontal cortex	UBERON:0000451	95.47	gold quality
left testis	UBERON:0004533	95.29	gold quality
nucleus accumbens	UBERON:0001882	95.27	gold quality
caudate nucleus	UBERON:0001873	95.17	gold quality
right testis	UBERON:0004534	95.17	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.15	gold quality
amygdala	UBERON:0001876	95.00	gold quality
adenohypophysis	UBERON:0002196	94.77	gold quality
cerebellar hemisphere	UBERON:0002245	94.62	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.62	gold quality
cerebellar cortex	UBERON:0002129	94.60	gold quality
putamen	UBERON:0001874	94.44	gold quality
paraflocculus	UBERON:0005351	93.56	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.56	gold quality
frontal pole	UBERON:0002795	93.42	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.30	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.27	gold quality
spinal cord	UBERON:0002240	93.24	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.06	gold quality
lower esophagus	UBERON:0013473	93.03	gold quality
cerebellum	UBERON:0002037	92.96	gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-GEOD-124263	yes	2099.75
E-MTAB-3929	yes	67.14
E-HCAD-10	yes	40.42
E-GEOD-125970	yes	7.07
E-CURD-112	yes	5.97
E-ANND-3	yes	5.18
E-MTAB-11121	no	827.58
E-HCAD-5	no	19.74
E-MTAB-8410	no	3.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting ZNF428, 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-8485	100.00	77.57	4731
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-3190-5P	98.87	64.89	1345
HSA-MIR-138-1-3P	98.25	67.89	867
HSA-MIR-4529-5P	96.74	65.77	569
HSA-MIR-6890-5P	92.89	65.83	442

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp428	ENSMUSG00000064264
rattus_norvegicus	Zfp428	ENSRNOG00000019802

Protein

Protein identifiers

Zinc finger protein 428 — Q96B54 (reviewed: Q96B54)

Alternative names: Enzyme-like protein PIT13

All UniProt accessions (2): Q96B54, M0QXZ5

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (1): NP_872304* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR038977	ZNF428	Family

UniProt features (8 total): compositionally biased region 4, chain 1, zinc finger region 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96B54-F1	61.99	0.14

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 (1): 108

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 99 (showing top): KOYAMA_SEMA3B_TARGETS_UP, POU3F2_02, BROWNE_HCMV_INFECTION_10HR_UP, OCT1_B, TTCNRGNNNNTTC_HSF_Q6, TCCCRNNRTGC_UNKNOWN, AHR_Q5, YATGNWAAT_OCT_C, HATADA_METHYLATED_IN_LUNG_CANCER_UP, OCT_Q6, RAO_BOUND_BY_SALL4_ISOFORM_B, ESC_V6.5_UP_LATE.V1_DN, RB_P130_DN.V1_UP, NRF1_Q6, ARNT2_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
binding	1
cation binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

316 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF428	UBL7	Q96S82	709
ZNF428	MAS1	P04201	691
ZNF428	CIAPIN1	Q6FI81	687
ZNF428	SLC44A3	Q8N4M1	656
ZNF428	M0R1W7	M0R1W7	591
ZNF428	RWDD1	Q9H446	518
ZNF428	CCDC97	Q96F63	476
ZNF428	GAGE10	A6NGK3	472
ZNF428	ASAH1	Q13510	472
ZNF428	MIEN1	Q9BRT3	471
ZNF428	ZNF668	Q96K58	459
ZNF428	ZBTB37	Q5TC79	448
ZNF428	MINDY3	Q9H8M7	414
ZNF428	CHAC2	Q8WUX2	413
ZNF428	IFT38	Q96AJ1	399

IntAct

15 interactions, top by confidence:

A	B	Type	Score
HMGB2	ZNF428	psi-mi:“MI:0915”(physical association)	0.670
ZNF428	HMGB1	psi-mi:“MI:0915”(physical association)	0.550
HMGB1	ZNF428	psi-mi:“MI:0915”(physical association)	0.550
ZNF428	PIP4K2A	psi-mi:“MI:0914”(association)	0.530
ZNF428	S100A10	psi-mi:“MI:0914”(association)	0.530
ZNF428	MACROH2A1	psi-mi:“MI:0914”(association)	0.350
ZNF428	ANXA2	psi-mi:“MI:0914”(association)	0.350
	TTC8	psi-mi:“MI:0914”(association)	0.350
	SRRM1	psi-mi:“MI:0914”(association)	0.350
PYHIN1	SUPT5H	psi-mi:“MI:0914”(association)	0.350

BioGRID (46): CHAMP1 (Affinity Capture-MS), POGZ (Affinity Capture-MS), FOXK2 (Affinity Capture-MS), FOXK1 (Affinity Capture-MS), HIST2H3PS2 (Affinity Capture-MS), PIP4K2C (Affinity Capture-MS), PARP2 (Affinity Capture-MS), PIP4K2B (Affinity Capture-MS), H2AFY (Affinity Capture-MS), GTF2I (Affinity Capture-MS), XPC (Affinity Capture-MS), HIST2H2AB (Affinity Capture-MS), PIP4K2A (Affinity Capture-MS), ACTBL2 (Affinity Capture-MS), ZNF428 (Two-hybrid)

ESM2 similar proteins: A0A2Z4LIS9, A1YG85, A2T756, A6NJT0, O08934, O15370, O70218, O70220, O89113, P09066, P0C7X2, P12980, P16443, P17542, P19622, P22091, P48435, P70061, P78367, P82976, P97503, Q04890, Q05916, Q05917, Q10586, Q14549, Q15270, Q32PF6, Q5VY09, Q60925, Q6IQX8, Q80WY3, Q8C1M2, Q8WY41, Q924A2, Q92949, Q96B54, Q96RK0, Q9BV97, Q9C009

Diamond homologs: Q8C1M2, Q96B54

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

713 predictions. Top by Δscore:

Variant	Effect	Δscore
19:43608103:GGGGC:G	acceptor_gain	1.0000
19:43608105:GGC:G	acceptor_gain	1.0000
19:43608106:GC:G	acceptor_gain	1.0000
19:43608107:CC:C	acceptor_gain	1.0000
19:43608108:C:CA	acceptor_loss	1.0000
19:43608108:C:CC	acceptor_gain	1.0000
19:43608109:T:A	acceptor_loss	1.0000
19:43614223:CCTTA:C	donor_loss	1.0000
19:43614224:CTTAC:C	donor_loss	1.0000
19:43614225:TTA:T	donor_loss	1.0000
19:43614227:ACCT:A	donor_loss	1.0000
19:43614228:C:G	donor_loss	1.0000
19:43619554:TCACC:T	donor_loss	1.0000
19:43619555:CACCG:C	donor_loss	1.0000
19:43619556:ACC:A	donor_loss	1.0000
19:43608104:GGGC:G	acceptor_gain	0.9900
19:43608119:C:CT	acceptor_gain	0.9900
19:43608120:A:T	acceptor_gain	0.9900
19:43608123:C:CT	acceptor_gain	0.9900
19:43614432:ATGC:A	acceptor_loss	0.9900
19:43614433:TG:T	acceptor_gain	0.9900
19:43614434:GCTG:G	acceptor_loss	0.9900
19:43614435:C:CA	acceptor_loss	0.9900
19:43614435:C:CC	acceptor_gain	0.9900
19:43614436:T:G	acceptor_loss	0.9900
19:43619550:ACACT:A	donor_loss	0.9900
19:43619551:CACTC:C	donor_loss	0.9900
19:43619552:ACTCA:A	donor_loss	0.9900
19:43619556:A:AC	donor_gain	0.9900
19:43619557:C:CC	donor_gain	0.9900

AlphaMissense

1205 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:43607645:A:G	F180S	0.999
19:43607697:A:G	C163R	0.999
19:43607644:G:C	F180L	0.998
19:43607644:G:T	F180L	0.998
19:43607646:A:G	F180L	0.998
19:43607674:G:C	F170L	0.998
19:43607674:G:T	F170L	0.998
19:43607676:A:G	F170L	0.998
19:43607687:C:G	C166S	0.998
19:43607688:A:T	C166S	0.998
19:43607695:A:C	C163W	0.998
19:43607696:C:G	C163S	0.998
19:43607696:C:T	C163Y	0.998
19:43607697:A:T	C163S	0.998
19:43607637:G:C	H183D	0.997
19:43607688:A:G	C166R	0.997
19:43607645:A:C	F180C	0.996
19:43607657:A:G	L176P	0.996
19:43607686:A:C	C166W	0.996
19:43607687:C:T	C166Y	0.996
19:43607635:A:C	H183Q	0.995
19:43607635:A:T	H183Q	0.995
19:43607637:G:T	H183N	0.995
19:43607647:G:C	H179Q	0.995
19:43607647:G:T	H179Q	0.995
19:43607687:C:A	C166F	0.995
19:43607696:C:A	C163F	0.995
19:43607675:A:G	F170S	0.994
19:43607633:G:T	A184D	0.993
19:43608003:A:G	Y61H	0.993

dbSNP variants (sampled 300 via entrez): RS1000087418 (19:43619999 C>T), RS1000164536 (19:43619643 G>A), RS1000401373 (19:43613417 C>A,T), RS1000644119 (19:43619548 G>A,C), RS1000812446 (19:43607002 G>A,C,T), RS1001004165 (19:43612530 A>C,G), RS1001050277 (19:43612736 G>A,T), RS1001099220 (19:43619166 GT>G), RS1001206258 (19:43610254 C>T), RS1001369007 (19:43608516 G>C), RS1001843306 (19:43612821 C>T), RS1001894451 (19:43619428 G>C), RS1001905305 (19:43620328 G>A,T), RS1001946947 (19:43619611 C>T), RS1001966681 (19:43619260 C>G,T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases methylation	5
sodium arsenite	affects cotreatment, increases abundance, decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, decreases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, decreases methylation	2
aristolochic acid I	increases expression	1
6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amine	decreases expression	1
ginger extract	increases abundance, decreases expression, decreases reaction	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	decreases expression, decreases reaction, increases abundance	1
beta-lapachone	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
potassium chromate(VI)	decreases expression	1
aflatoxin B2	increases methylation	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
di-n-butylphosphoric acid	affects expression	1
entinostat	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
LDN 193189	affects cotreatment, increases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	decreases expression, increases abundance, affects cotreatment	1
Cannabidiol	affects cotreatment, decreases expression	1
Cuprizone	affects cotreatment, decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Oils, Volatile	decreases expression, decreases reaction, increases abundance	1
Polychlorinated Biphenyls	affects expression	1
Potassium Dichromate	increases expression	1
Progesterone	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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