ZNF28

Summary

ZNF28 (zinc finger protein 28, HGNC:13073) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 28 (P17035). 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 7576 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 150 total
• MANE Select transcript: NM_006969

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13073
Approved symbol	ZNF28
Name	zinc finger protein 28
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Aliases	KOX24, DKFZp781D0275
Ensembl gene	ENSG00000198538
Ensembl biotype	protein_coding
OMIM	620466
Entrez	7576

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000339844, ENST00000391783, ENST00000438150, ENST00000457749, ENST00000464469, ENST00000542421, ENST00000594602, ENST00000596559, ENST00000868404

RefSeq mRNA: 8 — MANE Select: NM_006969 NM_001369761, NM_001369762, NM_001369763, NM_001369764, NM_001369765, NM_001369766, NM_001369768, NM_006969

CCDS: CCDS33093, CCDS92676, CCDS92677

Canonical transcript exons

ENST00000457749 — 4 exons

Exon	Start	End
ENSE00001471343	52821586	52821633
ENSE00003545254	52817944	52818031
ENSE00003671511	52808007	52808133
ENSE00003680409	52797408	52801702

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 86.06.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6436 / max 14.6347, expressed in 395 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182535	0.6436	395

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	86.06	gold quality
adrenal tissue	UBERON:0018303	86.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.82	gold quality
endometrium	UBERON:0001295	83.75	gold quality
colonic epithelium	UBERON:0000397	82.67	gold quality
ganglionic eminence	UBERON:0004023	82.40	gold quality
cortical plate	UBERON:0005343	82.38	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.89	gold quality
bone marrow cell	CL:0002092	80.85	gold quality
rectum	UBERON:0001052	80.72	gold quality
calcaneal tendon	UBERON:0003701	80.13	gold quality
ventricular zone	UBERON:0003053	79.82	gold quality
mucosa of transverse colon	UBERON:0004991	79.72	gold quality
tonsil	UBERON:0002372	79.62	gold quality
pancreas	UBERON:0001264	79.23	gold quality
granulocyte	CL:0000094	78.22	gold quality
leukocyte	CL:0000738	78.20	gold quality
stromal cell of endometrium	CL:0002255	78.01	gold quality
monocyte	CL:0000576	77.93	gold quality
placenta	UBERON:0001987	77.82	gold quality
adrenal gland	UBERON:0002369	77.72	gold quality
right adrenal gland cortex	UBERON:0035827	77.59	gold quality
duodenum	UBERON:0002114	77.56	gold quality
right adrenal gland	UBERON:0001233	77.45	gold quality
kidney	UBERON:0002113	77.17	gold quality
bone marrow	UBERON:0002371	77.08	gold quality
smooth muscle tissue	UBERON:0001135	76.97	gold quality
left adrenal gland	UBERON:0001234	76.93	gold quality
lymph node	UBERON:0000029	76.85	gold quality
gall bladder	UBERON:0002110	76.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.88

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

145 targeting ZNF28, 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-3064-3P	100.00	70.09	1254
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-12121	99.99	66.64	255
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-548J-3P	99.94	72.61	4881

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), 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 28 — P17035 (reviewed: P17035)

Alternative names: Zinc finger protein KOX24

All UniProt accessions (5): C9K0H3, P17035, F8WBV3, M0QXU3, M0R0U4

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 (2)

UniProt ID	Names	Canonical?
P17035-1	1	yes
P17035-2	2

RefSeq proteins (8): NP_001356690, NP_001356691, NP_001356692, NP_001356693, NP_001356694, NP_001356695, NP_001356697, NP_008900* (*=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, PF13465

UniProt features (34 total): zinc finger region 18, sequence conflict 8, sequence variant 3, cross-link 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17035-F1	69.35	0.20

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): 89, 428

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway
R-HSA-9843940	Regulation of endogenous retroelements by KRAB-ZFP proteins

MSigDB gene sets: 79 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ELF2_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF350_TARGET_GENES, ZNF362_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR548AJ_3P_MIR548X_3P, MIR4698, MIR548D_3P, MIR548H_3P_MIR548Z, MIR548BB_3P

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

GO Molecular Function (5): 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), metal ion binding (GO:0046872)

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

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
RNA Polymerase II Transcription	1
Regulation of endogenous retroelements	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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

352 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF28	A6NLF2	A6NLF2	515
ZNF28	A0A087WTG0	A0A087WTG0	507
ZNF28	NBPF26	B4DH59	507
ZNF28	CREG2	Q8IUH2	459
ZNF28	SREK1IP1	Q8N9Q2	457
ZNF28	SFXN3	Q9BWM7	450
ZNF28	LEMD3	Q9Y2U8	435
ZNF28	WIPF1	O43516	425
ZNF28	INSYN2B	A6NMK8	419
ZNF28	P2RX1	P51575	417
ZNF28	GNG12	Q9UBI6	396
ZNF28	FAM124A	Q86V42	390
ZNF28	PDE6B	P35913	387
ZNF28	CCDC43	Q96MW1	376
ZNF28	PMP2	P02689	363

IntAct

9 interactions, top by confidence:

A	B	Type	Score
MAPK6	HERC2	psi-mi:“MI:0914”(association)	0.840
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF28	TCAF1	psi-mi:“MI:0915”(physical association)	0.400
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): ZNF28 (Affinity Capture-MS), ZNF28 (Affinity Capture-MS), ZNF28 (Affinity Capture-MS), ZNF28 (Affinity Capture-MS), ZNF28 (Affinity Capture-RNA), ZNF28 (Affinity Capture-RNA), ZNF28 (Affinity Capture-MS), ZNF28 (Affinity Capture-MS), ZNF28 (Affinity Capture-MS), ZNF28 (Affinity Capture-MS)

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: A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	127
Likely benign	11
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1669 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52808046:C:A	donor_gain	1.0000
19:52818027:CAATC:C	acceptor_gain	1.0000
19:52818032:C:CC	acceptor_gain	1.0000
19:52849081:CCTCA:C	donor_loss	1.0000
19:52849082:CTCAC:C	donor_loss	1.0000
19:52849083:TCA:T	donor_loss	1.0000
19:52849084:CA:C	donor_loss	1.0000
19:52849085:AC:A	donor_gain	1.0000
19:52849086:CC:C	donor_gain	1.0000
19:52849126:C:A	donor_gain	1.0000
19:52849210:GACC:G	acceptor_gain	1.0000
19:52849211:ACCC:A	acceptor_loss	1.0000
19:52849212:CC:C	acceptor_gain	1.0000
19:52849213:CC:C	acceptor_gain	1.0000
19:52849213:CCTGA:C	acceptor_loss	1.0000
19:52849214:C:A	acceptor_loss	1.0000
19:52854252:TCTCA:T	donor_loss	1.0000
19:52854253:CTCA:C	donor_loss	1.0000
19:52854254:TCA:T	donor_loss	1.0000
19:52854255:CA:C	donor_loss	1.0000
19:52854256:ACCTG:A	donor_loss	1.0000
19:52854257:C:A	donor_loss	1.0000
19:52854341:CAATC:C	acceptor_gain	1.0000
19:52854344:TCC:T	acceptor_loss	1.0000
19:52854346:C:CC	acceptor_gain	1.0000
19:52854346:CTG:C	acceptor_loss	1.0000
19:52854347:T:C	acceptor_loss	1.0000
19:52808045:T:TA	donor_gain	0.9900
19:52808130:GACC:G	acceptor_gain	0.9900
19:52808132:CC:C	acceptor_gain	0.9900

AlphaMissense

4829 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:52800081:G:C	F588L	0.997
19:52800081:G:T	F588L	0.997
19:52800083:A:G	F588L	0.997
19:52799745:G:C	F700L	0.996
19:52799745:G:T	F700L	0.996
19:52799747:A:G	F700L	0.996
19:52799997:G:C	F616L	0.996
19:52799997:G:T	F616L	0.996
19:52799999:A:G	F616L	0.996
19:52799829:A:C	F672L	0.995
19:52799829:A:T	F672L	0.995
19:52799831:A:G	F672L	0.995
19:52800165:G:C	F560L	0.995
19:52800165:G:T	F560L	0.995
19:52800167:A:G	F560L	0.995
19:52800333:G:C	F504L	0.995
19:52800333:G:T	F504L	0.995
19:52800335:A:G	F504L	0.995
19:52799913:G:C	F644L	0.994
19:52799913:G:T	F644L	0.994
19:52799915:A:G	F644L	0.994
19:52800417:G:C	F476L	0.994
19:52800417:G:T	F476L	0.994
19:52800419:A:G	F476L	0.994
19:52800501:A:C	F448L	0.994
19:52800501:A:T	F448L	0.994
19:52800503:A:G	F448L	0.994
19:52800054:A:C	H597Q	0.993
19:52800054:A:T	H597Q	0.993
19:52800585:A:C	F420L	0.992

dbSNP variants (sampled 300 via entrez): RS1000023557 (19:52797426 A>C), RS1000077423 (19:52797694 A>C,T), RS1000097013 (19:52798556 T>C), RS1000150928 (19:52798254 C>T), RS1000457592 (19:52823011 A>C), RS1000723246 (19:52818318 T>C), RS1000849284 (19:52823198 A>C), RS1000863357 (19:52812867 A>T), RS1000918514 (19:52818661 C>A,G,T), RS1000963577 (19:52818521 T>C), RS1000978818 (19:52808629 C>A,G,T), RS1001096193 (19:52814206 C>A,G), RS1001247687 (19:52814317 A>G), RS1001305172 (19:52820501 G>A), RS1001315391 (19:52812538 G>A)

Disease associations

OMIM: gene MIM:620466 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002337_22	Amyotrophic lateral sclerosis (sporadic)	5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation, decreases methylation	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
sulforaphane	increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
bisphenol S	increases methylation	1
Arsenic Trioxide	increases expression, affects cotreatment	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	decreases expression	1
Doxorubicin	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Ozone	affects expression, increases abundance	1
Tretinoin	increases expression, affects cotreatment	1
Valproic Acid	increases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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