ZNF25

Summary

ZNF25 (zinc finger protein 25, HGNC:13043) is a protein-coding gene on chromosome 10p11.21, encoding Zinc finger protein 25 (P17030). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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 219749 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_145011

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13043
Approved symbol	ZNF25
Name	zinc finger protein 25
Location	10p11.21
Locus type	gene with protein product
Status	Approved
Aliases	KOX19, FLJ31890, Zfp9
Ensembl gene	ENSG00000175395
Ensembl biotype	protein_coding
OMIM	194528
Entrez	219749

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000302609, ENST00000374633, ENST00000467975, ENST00000897640, ENST00000897641, ENST00000897642, ENST00000897643, ENST00000897644, ENST00000963595, ENST00000963596, ENST00000963597, ENST00000963598

RefSeq mRNA: 19 — MANE Select: NM_145011 NM_001329647, NM_001329648, NM_001329649, NM_001329650, NM_001329651, NM_001329652, NM_001329653, NM_001329654, NM_001329655, NM_001329656, NM_001329657, NM_001329658, NM_001329659, NM_001329660, NM_001329661, NM_001329662, NM_001329663, NM_001329664, NM_145011

CCDS: CCDS7195

Canonical transcript exons

ENST00000302609 — 6 exons

Exon	Start	End
ENSE00001464116	37949573	37953195
ENSE00001921356	37976506	37976647
ENSE00003468135	37957420	37957546
ENSE00003488787	37953695	37953758
ENSE00003539721	37971708	37971807
ENSE00003652868	37957020	37957115

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 97.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.0525 / max 186.5970, expressed in 1259 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
109127	4.0067	1250
109126	0.0459	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	97.07	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.36	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.65	gold quality
substantia nigra pars compacta	UBERON:0001965	94.14	gold quality
primary visual cortex	UBERON:0002436	93.70	gold quality
vastus lateralis	UBERON:0001379	93.64	gold quality
occipital lobe	UBERON:0002021	93.46	gold quality
calcaneal tendon	UBERON:0003701	93.27	gold quality
quadriceps femoris	UBERON:0001377	93.02	gold quality
substantia nigra pars reticulata	UBERON:0001966	92.93	gold quality
lateral globus pallidus	UBERON:0002476	92.85	gold quality
pons	UBERON:0000988	92.77	gold quality
cortical plate	UBERON:0005343	92.58	gold quality
superior frontal gyrus	UBERON:0002661	92.25	gold quality
superior vestibular nucleus	UBERON:0007227	91.85	gold quality
tendon	UBERON:0000043	91.77	gold quality
deltoid	UBERON:0001476	91.64	gold quality
cerebellar vermis	UBERON:0004720	91.59	gold quality
parietal lobe	UBERON:0001872	91.49	gold quality
postcentral gyrus	UBERON:0002581	91.27	gold quality
biceps brachii	UBERON:0001507	91.18	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.01	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	90.95	gold quality
skeletal muscle tissue	UBERON:0001134	90.93	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.73	gold quality
ganglionic eminence	UBERON:0004023	90.71	gold quality
embryo	UBERON:0000922	90.70	gold quality
prefrontal cortex	UBERON:0000451	90.59	gold quality
frontal cortex	UBERON:0001870	90.21	gold quality
frontal lobe	UBERON:0016525	90.21	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.56

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

123 targeting ZNF25, 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-3120-5P	100.00	65.56	965
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-218-5P	99.93	72.22	2103

Literature-anchored findings (GeneRIF, showing 1)

• This study shows that the uncharacterized transcription factor, ZNF25, is associated with differentiation of hMSC to osteoblasts. (PMID:27814695)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp9	ENSMUSG00000072623
rattus_norvegicus	Zfp9	ENSRNOG00000006726
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), ZNF589 (ENSG00000164048), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 25 — P17030 (reviewed: P17030)

Alternative names: Zinc finger protein KOX19

All UniProt accessions (1): P17030

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?
P17030-1	1	yes
P17030-2	2

RefSeq proteins (19): NP_001316576, NP_001316577, NP_001316578, NP_001316579, NP_001316580, NP_001316581, NP_001316582, NP_001316583, NP_001316584, NP_001316585, NP_001316586, NP_001316587, NP_001316588, NP_001316589, NP_001316590, NP_001316591, NP_001316592, NP_001316593, NP_659448* (*=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF01352

UniProt features (19 total): zinc finger region 12, sequence variant 3, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17030-F1	78.64	0.41

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 58 (showing top): GTGCCTT_MIR506, chr10p11, CTGTTAC_MIR194, GCACTTT_MIR175P_MIR20A_MIR106A_MIR106B_MIR20B_MIR519D, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, FEV_TARGET_GENES, NKX2_2_TARGET_GENES, SALL4_TARGET_GENES, ZIM3_TARGET_GENES, ZNF8_TARGET_GENES, MIR106B_5P, MIR20A_5P, MIR106A_5P, MIR17_5P

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

GO Molecular Function (6): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), 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
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

462 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF25	RASGEF1C	Q8N431	400
ZNF25	MTRNR2L7	P0CJ74	370
ZNF25	BRD8	Q9H0E9	367
ZNF25	ZNF608	Q9ULD9	357
ZNF25	RANBP3L	Q86VV4	348
ZNF25	ZZZ3	Q8IYH5	338
ZNF25	ZSWIM3	Q96MP5	318
ZNF25	ZBTB21	Q9ULJ3	316
ZNF25	ZNHIT1	O43257	314
ZNF25	SMARCC2	Q8TAQ2	314
ZNF25	ZFAND3	Q9H8U3	306
ZNF25	PHYHIPL	Q96FC7	285
ZNF25	COMTD1	Q86VU5	264
ZNF25	NFIX	Q14938	257
ZNF25	TAF1A	Q15573	255

IntAct

6 interactions, top by confidence:

A	B	Type	Score
HEMGN	NPM1	psi-mi:“MI:0914”(association)	0.600
ZNF25	SCRN1	psi-mi:“MI:0915”(physical association)	0.560
ZNF25	ADRB2	psi-mi:“MI:0915”(physical association)	0.370
SCRN1	ZNF25	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): ZNF25 (Two-hybrid), ZNF25 (Two-hybrid), ZNF25 (Two-hybrid), ZNF25 (Affinity Capture-MS), ZNF25 (Affinity Capture-MS)

ESM2 similar proteins: A2RRD8, A6NHJ4, A6NK75, B4DU55, O75346, P0DPD5, P15621, P17030, P17039, P52737, Q0VGE8, Q14588, Q147U1, Q15928, Q2M3X9, Q3KNS6, Q494X3, Q4R6C2, Q5HYK9, Q5R5Q6, Q5R5S6, Q5REA0, Q5REK1, Q60585, Q61751, Q6ECI4, Q6P9Y7, Q6ZN19, Q6ZNA1, Q7Z3V5, Q86T29, Q86WZ6, Q8N141, Q8N7K0, Q8N9F8, Q8NA42, Q8NCK3, Q8NDQ6, Q8NEM1, Q8WV37

Diamond homologs: A0A1W2PQL4, A0JNB1, A0JPL0, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MT65, A8MUV8, A8MWA4, B2RXC5, B4DU55, B4DX44, E9PYI1, O14628, O75346, P0CH99, P0CI00, P17014, P17030, P17032, P17098, P51786, P85977, Q02386, Q06730, Q06732, Q0VAW7, Q12901, Q13360, Q14586, Q14588, Q14590, Q16587, Q2M3X9, Q2VY69, Q32M78, Q3ZCX4, Q49AA0, Q4R6J4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1417 predictions. Top by Δscore:

Variant	Effect	Δscore
10:37957114:ACC:A	acceptor_loss	1.0000
10:37957115:CCTAT:C	acceptor_loss	1.0000
10:37957116:C:CA	acceptor_loss	1.0000
10:37957419:CCCA:C	donor_gain	1.0000
10:37957422:A:AC	donor_gain	1.0000
10:37957423:C:CC	donor_gain	1.0000
10:37957458:T:TA	donor_gain	1.0000
10:37971703:CTCA:C	donor_loss	1.0000
10:37971704:TCA:T	donor_loss	1.0000
10:37971705:CA:C	donor_loss	1.0000
10:37971706:A:AG	donor_loss	1.0000
10:37975035:A:AC	donor_gain	1.0000
10:37975036:C:CC	donor_gain	1.0000
10:37953756:CTT:C	acceptor_gain	0.9900
10:37953759:C:CC	acceptor_gain	0.9900
10:37957116:C:CC	acceptor_gain	0.9900
10:37967957:C:CT	acceptor_gain	0.9900
10:37970292:AC:A	donor_gain	0.9900
10:37970293:CC:C	donor_gain	0.9900
10:37971806:ACCT:A	acceptor_loss	0.9900
10:37971807:CCTGT:C	acceptor_loss	0.9900
10:37971808:C:CG	acceptor_loss	0.9900
10:37971809:T:G	acceptor_loss	0.9900
10:37975036:CT:C	donor_gain	0.9900
10:37953757:TT:T	acceptor_gain	0.9800
10:37953758:TC:T	acceptor_loss	0.9800
10:37953759:CTACA:C	acceptor_loss	0.9800
10:37953760:T:A	acceptor_loss	0.9800
10:37957385:C:CT	donor_gain	0.9800
10:37957386:T:TT	donor_gain	0.9800

AlphaMissense

3047 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:37952361:A:C	F379L	0.997
10:37952361:A:T	F379L	0.997
10:37952363:A:G	F379L	0.997
10:37952697:A:C	F267L	0.997
10:37952697:A:T	F267L	0.997
10:37952699:A:G	F267L	0.997
10:37952680:A:G	L273P	0.996
10:37952428:A:G	L357P	0.995
10:37952497:C:G	R334P	0.995
10:37952277:A:C	F407L	0.994
10:37952277:A:T	F407L	0.994
10:37952279:A:G	F407L	0.994
10:37952445:A:C	F351L	0.993
10:37952445:A:T	F351L	0.993
10:37952447:A:G	F351L	0.993
10:37952596:A:G	L301P	0.993
10:37952529:G:C	F323L	0.992
10:37952529:G:T	F323L	0.992
10:37952531:A:G	F323L	0.992
10:37952613:G:C	F295L	0.992
10:37952613:G:T	F295L	0.992
10:37952615:A:G	F295L	0.992
10:37952332:T:G	Q389P	0.991
10:37952764:A:G	L245P	0.991
10:37952865:G:C	F211L	0.991
10:37952865:G:T	F211L	0.991
10:37952867:A:G	F211L	0.991
10:37952272:T:G	Q409P	0.990
10:37952848:A:G	L217P	0.990
10:37952248:T:G	Q417P	0.989

dbSNP variants (sampled 300 via entrez): RS1000270229 (10:37958111 A>G), RS1000271825 (10:37967009 A>G), RS1000301271 (10:37957883 T>C,G), RS1000302864 (10:37966706 A>T), RS1000350225 (10:37953607 T>C), RS1000423436 (10:37974505 A>C,G), RS1000542461 (10:37978274 G>A), RS1000606857 (10:37959845 G>A), RS1000863817 (10:37951589 T>C), RS1001187812 (10:37963803 T>C), RS1001226983 (10:37972659 A>T), RS1001397136 (10:37960900 T>A,C), RS1001514378 (10:37978566 T>C), RS1001629582 (10:37959792 T>C), RS1001662464 (10:37959467 C>T)

Disease associations

OMIM: gene MIM:194528 | 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
GCST005288_3	Extrinsic epigenetic age acceleration	1.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0000473	epigenetic status
EFO:0022597	aging

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression	3
Cyclosporine	increases expression	3
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
perfluorooctanoic acid	increases expression	1
zinc chromate	increases abundance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	increases abundance, increases expression	1
perfluorooctane sulfonic acid	increases expression	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Fulvestrant	increases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Doxorubicin	decreases expression	1
Niclosamide	increases expression	1
Phthalic Acids	decreases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Antirheumatic Agents	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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