ZNF728

Summary

ZNF728 (zinc finger protein 728, HGNC:32463) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 728 (P0DKX0).

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 388523 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001267716

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32463
Approved symbol	ZNF728
Name	zinc finger protein 728
Location	19p12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000269067
Ensembl biotype	protein_coding
Entrez	388523

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000594710, ENST00000599851

RefSeq mRNA: 1 — MANE Select: NM_001267716 NM_001267716

CCDS: CCDS59370

Canonical transcript exons

ENST00000594710 — 4 exons

Exon	Start	End
ENSE00002985898	22987308	22987403
ENSE00003087098	22974883	22977110
ENSE00003094229	23003028	23003176
ENSE00003180307	22988325	22988451

Expression profiles

Bgee: expression breadth ubiquitous, 117 present calls, max score 82.44.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7062 / max 86.9228, expressed in 186 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180260	0.6532	182
180259	0.0529	25

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.44	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.34	gold quality
testis	UBERON:0000473	71.19	gold quality
right testis	UBERON:0004534	70.51	gold quality
corpus callosum	UBERON:0002336	70.01	gold quality
left testis	UBERON:0004533	69.71	gold quality
smooth muscle tissue	UBERON:0001135	64.68	gold quality
heart left ventricle	UBERON:0002084	62.66	gold quality
heart	UBERON:0000948	62.02	gold quality
right atrium auricular region	UBERON:0006631	61.37	gold quality
islet of Langerhans	UBERON:0000006	59.43	gold quality
apex of heart	UBERON:0002098	58.23	gold quality
fallopian tube	UBERON:0003889	58.09	gold quality
descending thoracic aorta	UBERON:0002345	57.98	gold quality
lower esophagus muscularis layer	UBERON:0035833	57.87	gold quality
lower esophagus	UBERON:0013473	57.82	gold quality
calcaneal tendon	UBERON:0003701	57.28	gold quality
right coronary artery	UBERON:0001625	57.19	gold quality
ovary	UBERON:0000992	56.94	gold quality
left ovary	UBERON:0002119	56.84	gold quality
thoracic aorta	UBERON:0001515	56.56	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	56.48	gold quality
ascending aorta	UBERON:0001496	56.40	gold quality
left coronary artery	UBERON:0001626	56.27	gold quality
urinary bladder	UBERON:0001255	56.26	gold quality
myometrium	UBERON:0001296	56.16	gold quality
gall bladder	UBERON:0002110	55.26	gold quality
left uterine tube	UBERON:0001303	55.10	gold quality
body of uterus	UBERON:0009853	54.36	gold quality
caudate nucleus	UBERON:0001873	54.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.27

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2589.1	ZNF728	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605368

miRNA regulators (miRDB)

56 targeting ZNF728, 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-3925-3P	100.00	69.95	1237
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-12121	99.99	66.64	255
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3658	99.96	73.87	4379
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-6809-3P	99.91	71.45	3814
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-325	99.58	66.55	358
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-486-5P	99.51	70.39	707
HSA-MIR-1224-5P	99.48	65.59	803
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-21-5P	99.46	70.54	1035
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-590-5P	99.25	70.76	930
HSA-MIR-8065	99.19	70.38	1289

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 728 — P0DKX0 (reviewed: P0DKX0)

All UniProt accessions (2): P0DKX0, M0QZ07

RefSeq proteins (1): NP_001254645* (*=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
IPR050329	GLI_C2H2-zinc-finger	Family

Pfam: PF00096, PF01352, PF13465, PF13912

UniProt features (16 total): zinc finger region 14, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DKX0-F1	69.18	0.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): chr19p12, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, TRIP13_TARGET_GENES, MIR6833_3P, MIR6873_3P, MIR4768_5P, MIR892C_5P, MIR3925_3P, MIR3064_3P, MIR4511, MIR4776_3P

GO Biological Process (4): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944), 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), transcription cis-regulatory region binding (GO:0000976), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nuclear lumen (GO:0031981)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	3
transcription by RNA polymerase II	3
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
negative regulation of DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of DNA-templated transcription	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
transition metal ion binding	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nucleus	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

198 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF728	CFAP96	A7E2U8	503
ZNF728	ESRP1	Q6NXG1	454
ZNF728	NFYB	P25208	447
ZNF728	TTC29	Q8NA56	393
ZNF728	DNAH11	Q96DT5	378
ZNF728	DMRTC2	Q8IXT2	359
ZNF728	ZGLP1	P0C6A0	358
ZNF728	ICA1L	Q8NDH6	353
ZNF728	CYP20A1	Q6UW02	350
ZNF728	GK5	Q6ZS86	328
ZNF728	ANKRD28	O15084	303
ZNF728	RP1L1	Q8IWN7	267
ZNF728	LOXHD1	Q8IVV2	261
ZNF728	CWC22	Q9HCG8	257
ZNF728	SIX2	Q9NPC8	254

IntAct

0 interactions, top by confidence:

BioGRID (3): ZNF728 (Positive Genetic), ZNF728 (Affinity Capture-MS), ZNF728 (Proximity Label-MS)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

719 predictions. Top by Δscore:

Variant	Effect	Δscore
19:22977111:C:CC	acceptor_gain	1.0000
19:22988364:T:A	donor_gain	1.0000
19:22988447:GATCC:G	acceptor_gain	1.0000
19:22988449:TCC:T	acceptor_gain	1.0000
19:22988450:CC:C	acceptor_gain	1.0000
19:22988450:CCC:C	acceptor_gain	1.0000
19:22988451:CC:C	acceptor_gain	1.0000
19:22988451:CCTG:C	acceptor_loss	1.0000
19:22988452:C:CA	acceptor_loss	1.0000
19:22988452:C:CC	acceptor_gain	1.0000
19:22988453:T:A	acceptor_loss	1.0000
19:23003024:TCAC:T	donor_loss	1.0000
19:23003025:CA:C	donor_loss	1.0000
19:23003026:A:C	donor_loss	1.0000
19:22977106:TATAA:T	acceptor_gain	0.9900
19:22977107:ATAA:A	acceptor_gain	0.9900
19:22977108:TAA:T	acceptor_gain	0.9900
19:22977572:G:C	donor_gain	0.9900
19:22988319:TCTCA:T	donor_loss	0.9900
19:22988320:CTCA:C	donor_loss	0.9900
19:22988321:TCA:T	donor_loss	0.9900
19:22988322:C:CG	donor_loss	0.9900
19:22988323:A:AC	donor_gain	0.9900
19:22988323:A:C	donor_loss	0.9900
19:22988323:AC:A	donor_gain	0.9900
19:22988324:C:CC	donor_gain	0.9900
19:22988324:CC:C	donor_gain	0.9900
19:22988448:ATCC:A	acceptor_gain	0.9900
19:23003026:A:AC	donor_gain	0.9900
19:23003026:AC:A	donor_gain	0.9900

AlphaMissense

4148 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:22975786:G:C	F517L	0.987
19:22975786:G:T	F517L	0.987
19:22975788:A:G	F517L	0.987
19:22975618:A:C	F573L	0.985
19:22975618:A:T	F573L	0.985
19:22975620:A:G	F573L	0.985
19:22976458:A:C	F293L	0.983
19:22976458:A:T	F293L	0.983
19:22976460:A:G	F293L	0.983
19:22976206:G:C	F377L	0.982
19:22976206:G:T	F377L	0.982
19:22976208:A:G	F377L	0.982
19:22976374:G:C	F321L	0.978
19:22976374:G:T	F321L	0.978
19:22976376:A:G	F321L	0.978
19:22975702:G:C	F545L	0.977
19:22975702:G:T	F545L	0.977
19:22975704:A:G	F545L	0.977
19:22976542:G:C	F265L	0.970
19:22976542:G:T	F265L	0.970
19:22976544:A:G	F265L	0.970
19:22975870:A:C	F489L	0.968
19:22975870:A:T	F489L	0.968
19:22975872:A:G	F489L	0.968
19:22976038:A:C	F433L	0.966
19:22976038:A:T	F433L	0.966
19:22976040:A:G	F433L	0.966
19:22976290:A:C	F349L	0.965
19:22976290:A:T	F349L	0.965
19:22976292:A:G	F349L	0.965

dbSNP variants (sampled 300 via entrez): RS1000010482 (19:22998216 G>C), RS1000064182 (19:22997998 C>T), RS1000334976 (19:23003330 A>G,T), RS1001040311 (19:22978911 G>A), RS1001052970 (19:22979275 T>A), RS1001087815 (19:22985913 C>A), RS1001369740 (19:22991514 G>T), RS1001426119 (19:22984277 G>A), RS1001450099 (19:22978567 G>C), RS1001732689 (19:22996380 C>A,T), RS1002032102 (19:22995057 T>C,G), RS1002359542 (19:23000963 CAT>C), RS1002433197 (19:22988778 G>A,T), RS1002682548 (19:23005028 G>A), RS1002870736 (19:22982471 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

2 associations (top):

Study	Trait	p-value
GCST002104_26	Bronchopulmonary dysplasia	4.000000e-06
GCST004713_9	Testicular germ cell tumor	5.000000e-14

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
FR900359	increases phosphorylation	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Cadmium	increases abundance, increases expression	1
Manganese	increases expression, affects cotreatment, increases abundance	1
Tetrachlorodibenzodioxin	affects expression	1

Clinical trials (associated diseases)

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